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X-ray Crystal Structure of Pseudoazurin Met16Gly variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YL4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.1 M HEPES, 42 %(w/v) PEG200
Crystal Properties Matthews coefficient Solvent content 1.89 34.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.181 α = 90 b = 53.014 β = 90 c = 59.114 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 PIXEL DECTRIS EIGER X 16M 2022-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.999870 SLS X06SA
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 1.2 39.47 99.9 0.055 0.065 0.035 0.996 21.6 6.3 31352
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.22 0.305 0.362 0.192 0.959 8.1 6.3
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.2 39.47 31296 1567 99.758 0.132 0.1311 0.1526 0.1947 10.593
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] 0.822 -0.201 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.186 r_lrange_it 12.995 r_dihedral_angle_3_deg 12.22 r_lrange_other 11.917 r_scangle_it 7.297 r_scangle_other 7.292 r_dihedral_angle_1_deg 6.721 r_mcangle_it 5.652 r_mcangle_other 5.652 r_dihedral_angle_2_deg 5.205
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.186 r_lrange_it 12.995 r_dihedral_angle_3_deg 12.22 r_lrange_other 11.917 r_scangle_it 7.297 r_scangle_other 7.292 r_dihedral_angle_1_deg 6.721 r_mcangle_it 5.652 r_mcangle_other 5.652 r_dihedral_angle_2_deg 5.205 r_scbond_it 5.088 r_scbond_other 5.084 r_rigid_bond_restr 3.865 r_mcbond_it 3.792 r_mcbond_other 3.784 r_angle_refined_deg 1.986 r_angle_other_deg 0.616 r_symmetry_nbd_refined 0.396 r_nbd_other 0.286 r_nbd_refined 0.268 r_xyhbond_nbd_refined 0.221 r_symmetry_nbd_other 0.204 r_symmetry_xyhbond_nbd_refined 0.204 r_nbtor_refined 0.178 r_metal_ion_refined 0.151 r_chiral_restr 0.099 r_symmetry_nbtor_other 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 909 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction MOLREP phasing