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Crystal Structure of SilF Cu(I)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8BBZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.2M potassium sodium tartrate tetrahydrate & 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.7 54.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.297 α = 90 b = 77.297 β = 90 c = 187.69 γ = 90
Symmetry Space Group I 21 21 21
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 PILATUS3 6M 2020-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.999 Diamond I24
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 2.2 47.275 99.9 0.997 7.8 24.2 28978 43.13
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 2.2 2.2 99.4 0.901 1.8 16.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.2 47.275 28978 1427 99.91 0.281 0.2797 0.2825 0.2986 0.2949 55.098
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] 0.136 0.047 -0.183
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.247 r_dihedral_angle_6_deg 14.509 r_lrange_it 11.526 r_lrange_other 11.525 r_scangle_it 9.57 r_scangle_other 9.568 r_mcangle_it 8.094 r_mcangle_other 8.094 r_dihedral_angle_2_deg 7.036 r_dihedral_angle_1_deg 6.783
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.247 r_dihedral_angle_6_deg 14.509 r_lrange_it 11.526 r_lrange_other 11.525 r_scangle_it 9.57 r_scangle_other 9.568 r_mcangle_it 8.094 r_mcangle_other 8.094 r_dihedral_angle_2_deg 7.036 r_dihedral_angle_1_deg 6.783 r_scbond_it 6.238 r_scbond_other 6.236 r_mcbond_it 5.34 r_mcbond_other 5.334 r_angle_refined_deg 1.44 r_angle_other_deg 0.502 r_symmetry_nbd_refined 0.317 r_nbd_other 0.223 r_metal_ion_refined 0.219 r_nbd_refined 0.208 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.168 r_symmetry_xyhbond_nbd_refined 0.147 r_ncsr_local_group_1 0.127 r_ncsr_local_group_6 0.124 r_xyhbond_nbd_refined 0.122 r_ncsr_local_group_10 0.116 r_ncsr_local_group_8 0.112 r_ncsr_local_group_11 0.111 r_ncsr_local_group_5 0.109 r_ncsr_local_group_3 0.108 r_ncsr_local_group_9 0.107 r_ncsr_local_group_12 0.106 r_ncsr_local_group_4 0.104 r_ncsr_local_group_13 0.099 r_ncsr_local_group_14 0.088 r_symmetry_nbtor_other 0.086 r_ncsr_local_group_7 0.08 r_ncsr_local_group_15 0.078 r_ncsr_local_group_2 0.071 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3634 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing