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X-ray structure of the K72I,Y129F,R133L, H199A quadruple mutant of PNP-oxidase from E. coli
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 2.88 57.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.776 α = 90 b = 63.776 β = 90 c = 124.727 γ = 120
Symmetry Space Group P 31 2 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 PILATUS3 6M 2020-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.968620 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.558 55.233 98 0.13 0.134 0.03 0.999 13.6 19.7 41877
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 1.558 1.585 98 0.803 0.444 0.9 11.91
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 1.558 55.232 41608 2061 97.351 0.172 0.1706 0.1818 0.2022 0.2128 33.06
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] 0.778 0.389 0.778 -2.524
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.336 r_dihedral_angle_3_deg 13.685 r_dihedral_angle_4_deg 13.185 r_lrange_it 8.08 r_lrange_other 7.994 r_dihedral_angle_1_deg 7.082 r_scangle_it 6.075 r_scangle_other 6.061 r_mcangle_other 4.181 r_mcangle_it 4.178
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.336 r_dihedral_angle_3_deg 13.685 r_dihedral_angle_4_deg 13.185 r_lrange_it 8.08 r_lrange_other 7.994 r_dihedral_angle_1_deg 7.082 r_scangle_it 6.075 r_scangle_other 6.061 r_mcangle_other 4.181 r_mcangle_it 4.178 r_scbond_it 4.036 r_scbond_other 3.972 r_mcbond_it 3.017 r_mcbond_other 3.008 r_angle_refined_deg 1.721 r_angle_other_deg 1.428 r_nbd_refined 0.272 r_xyhbond_nbd_refined 0.237 r_symmetry_xyhbond_nbd_refined 0.204 r_symmetry_nbd_other 0.196 r_nbd_other 0.193 r_nbtor_refined 0.175 r_symmetry_nbd_refined 0.173 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.083 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1748 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 46
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