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X-ray Crystal Structure of Pseudoazurin Met16Arg variant, oxidized form at pH 7.0
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, SITTING DROP 7 298 PEG1500, 100 mM potassium phosphate
Crystal Properties Matthews coefficient Solvent content 2.11 41.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.164 α = 90 b = 60.11 β = 106.568 c = 54.345 γ = 90
Symmetry Space Group P 1 21 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 PILATUS4 X 1M 2023-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.033200 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 1.22 39.37 95.9 0.042 0.06 0.042 0.992 9.4 2.3 61638
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 1.22 1.24 99 0.279 0.387 0.268 0.557 2 2.2
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 1.22 33.727 61615 3177 95.557 0.182 0.1808 0.1899 0.2112 0.2208 12.23
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] 1.202 -0.057 -1.044 -0.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.804 r_dihedral_angle_2_deg 12.947 r_dihedral_angle_3_deg 12.702 r_lrange_it 9.668 r_lrange_other 8.79 r_dihedral_angle_1_deg 7.166 r_rigid_bond_restr 3.041 r_angle_refined_deg 1.947 r_scangle_it 1.578 r_scangle_other 1.457
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.804 r_dihedral_angle_2_deg 12.947 r_dihedral_angle_3_deg 12.702 r_lrange_it 9.668 r_lrange_other 8.79 r_dihedral_angle_1_deg 7.166 r_rigid_bond_restr 3.041 r_angle_refined_deg 1.947 r_scangle_it 1.578 r_scangle_other 1.457 r_scbond_it 1.089 r_mcangle_other 1.047 r_mcangle_it 1.046 r_scbond_other 0.967 r_mcbond_it 0.642 r_mcbond_other 0.638 r_angle_other_deg 0.636 r_xyhbond_nbd_refined 0.27 r_symmetry_nbd_refined 0.251 r_nbd_refined 0.221 r_xyhbond_nbd_other 0.211 r_symmetry_nbd_other 0.199 r_symmetry_xyhbond_nbd_refined 0.199 r_nbd_other 0.184 r_nbtor_refined 0.175 r_metal_ion_refined 0.168 r_chiral_restr 0.098 r_symmetry_nbtor_other 0.085 r_symmetry_xyhbond_nbd_other 0.044 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1832 Nucleic Acid Atoms Solvent Atoms 474 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing