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Crystal structure of the branched-chain polyamine synthase (BpsA) from Thermococcus kodakarensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QM3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 293 100mM NaCl, 100mM lithium sulfate, 100mM ADA (pH6.5), 11.5% (w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.35 47.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.661 α = 90 b = 105.167 β = 90 c = 80.888 γ = 90
Symmetry Space Group P 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 CCD RAYONIX MX300HE 2014-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9000 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 50 100 0.109 23.6 14.6 60904
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 100 1.3 14.3
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2QM3 1.9 50 57839 2991 99.8 0.205 0.203 0.244 0.2344 RANDOM 42.83
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] -2.14 -2.65 4.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.652 r_dihedral_angle_3_deg 16.311 r_dihedral_angle_4_deg 15.219 r_long_range_B_other 10.411 r_long_range_B_refined 10.395 r_dihedral_angle_1_deg 6.374 r_scangle_other 4.963 r_mcangle_other 3.102 r_mcangle_it 3.1 r_scbond_it 3.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.652 r_dihedral_angle_3_deg 16.311 r_dihedral_angle_4_deg 15.219 r_long_range_B_other 10.411 r_long_range_B_refined 10.395 r_dihedral_angle_1_deg 6.374 r_scangle_other 4.963 r_mcangle_other 3.102 r_mcangle_it 3.1 r_scbond_it 3.087 r_scbond_other 3.086 r_angle_refined_deg 2.164 r_mcbond_it 2.054 r_mcbond_other 2.044 r_angle_other_deg 1.257 r_chiral_restr 0.138 r_bond_refined_d 0.024 r_gen_planes_refined 0.011 r_bond_other_d 0.005 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5670 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing