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X-ray structure of the K72I, Y129F, R133L, H199A quadruple mutant of PNP-oxidase from E. coli in complex with PLP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G76
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 100 mM KPHO pH 7,5, 5 mM 2-mercaptoethanol, 150 mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.26 45.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.164 α = 90 b = 54.164 β = 90 c = 271.968 γ = 120
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 2019-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96828 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 2.417 46.907 100 0.217 0.048 0.999 11.9 20.1 17206
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.417 2.459 100 0.875 0.392 0.9 17.2
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 1G76 2.417 46.907 17189 800 99.895 0.193 0.1897 0.1983 0.2588 0.2585 59.324
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] -1.799 -0.9 -1.799 5.836
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.122 r_dihedral_angle_4_deg 16.91 r_dihedral_angle_3_deg 16.859 r_lrange_it 7.621 r_lrange_other 7.621 r_dihedral_angle_1_deg 6.864 r_scangle_it 5.2 r_scangle_other 5.199 r_mcangle_it 4.814 r_mcangle_other 4.814
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.122 r_dihedral_angle_4_deg 16.91 r_dihedral_angle_3_deg 16.859 r_lrange_it 7.621 r_lrange_other 7.621 r_dihedral_angle_1_deg 6.864 r_scangle_it 5.2 r_scangle_other 5.199 r_mcangle_it 4.814 r_mcangle_other 4.814 r_scbond_it 3.169 r_scbond_other 3.163 r_mcbond_it 3.055 r_mcbond_other 3.053 r_angle_other_deg 2.237 r_angle_refined_deg 1.784 r_nbd_other 0.229 r_symmetry_nbd_other 0.196 r_symmetry_nbd_refined 0.194 r_nbd_refined 0.181 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.158 r_symmetry_xyhbond_nbd_refined 0.141 r_chiral_restr 0.115 r_xyhbond_nbd_other 0.084 r_symmetry_nbtor_other 0.078 r_symmetry_xyhbond_nbd_other 0.069 r_bond_other_d 0.034 r_bond_refined_d 0.014 r_gen_planes_other 0.006 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2925 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement autoPROC data collection autoPROC data processing XDS data reduction XDS data scaling Aimless data processing MOLREP phasing Coot model building