☰ Navigation Tabs
Crystal structure of the Q65N mutant of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa crystallized in the presence of K+ cations
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6F3M 6F3M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 50 mM KH2PO4, 20% (w/v) PEG8000, 20% (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 3.07 59.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.481 α = 90 b = 211.877 β = 105.325 c = 111.351 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2021-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9762 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.9 95.879 99 0.997 9.72 6.622 453838
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.95 0.593
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6F3M 1.9 95.879 386694 1163 99.214 0.16 0.1604 0.1665 0.1938 0.2023 36.115
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -7.686 -0.554 17.862 -10.176
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.917 r_dihedral_angle_4_deg 16.942 r_dihedral_angle_3_deg 14.256 r_dihedral_angle_1_deg 7.822 r_lrange_it 4.466 r_lrange_other 4.466 r_scangle_it 3.35 r_scangle_other 3.35 r_scbond_it 2.761 r_scbond_other 2.761
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.917 r_dihedral_angle_4_deg 16.942 r_dihedral_angle_3_deg 14.256 r_dihedral_angle_1_deg 7.822 r_lrange_it 4.466 r_lrange_other 4.466 r_scangle_it 3.35 r_scangle_other 3.35 r_scbond_it 2.761 r_scbond_other 2.761 r_mcangle_it 2.717 r_mcangle_other 2.717 r_mcbond_it 2.422 r_mcbond_other 2.422 r_angle_refined_deg 1.53 r_angle_other_deg 1.325 r_xyhbond_nbd_refined 0.225 r_symmetry_xyhbond_nbd_refined 0.206 r_nbd_refined 0.204 r_symmetry_nbd_refined 0.203 r_nbd_other 0.192 r_symmetry_nbd_other 0.181 r_nbtor_refined 0.154 r_symmetry_xyhbond_nbd_other 0.15 r_chiral_restr 0.092 r_metal_ion_refined 0.084 r_symmetry_nbtor_other 0.079 r_ncsr_local_group_20 0.068 r_ncsr_local_group_19 0.066 r_ncsr_local_group_7 0.065 r_ncsr_local_group_27 0.064 r_ncsr_local_group_28 0.064 r_ncsr_local_group_3 0.063 r_ncsr_local_group_21 0.063 r_ncsr_local_group_23 0.063 r_ncsr_local_group_25 0.063 r_ncsr_local_group_5 0.062 r_ncsr_local_group_26 0.062 r_ncsr_local_group_16 0.061 r_ncsr_local_group_1 0.059 r_ncsr_local_group_18 0.059 r_ncsr_local_group_2 0.058 r_ncsr_local_group_13 0.058 r_ncsr_local_group_24 0.058 r_ncsr_local_group_6 0.057 r_ncsr_local_group_10 0.057 r_ncsr_local_group_12 0.057 r_ncsr_local_group_14 0.055 r_ncsr_local_group_4 0.054 r_ncsr_local_group_8 0.054 r_ncsr_local_group_9 0.054 r_ncsr_local_group_15 0.054 r_ncsr_local_group_22 0.052 r_ncsr_local_group_11 0.048 r_ncsr_local_group_17 0.046 r_gen_planes_refined 0.014 r_bond_refined_d 0.012 r_gen_planes_other 0.002 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28408 Nucleic Acid Atoms Solvent Atoms 2820 Heterogen Atoms 559
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing