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X-ray Crystal Structure of Pseudoazurin Met16Ala variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8WQZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 298 0.1 M Tris-HCl, 37% (w/v) PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.15 42.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.086 α = 90 b = 59.841 β = 93.84 c = 109.767 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 EIGER X 4M 2025-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.0070 Photon Factory BL-1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.8 40.43 98.2 0.991 8 3 40219
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 99.2 0.799 2.7 3.1
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 1.8 40.43 40195 2088 98.053 0.168 0.1653 0.1722 0.2254 0.2228 15.637
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] 0.288 -0.379 -0.07 -0.166
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.809 r_dihedral_angle_3_deg 12.024 r_dihedral_angle_1_deg 7.05 r_lrange_it 5.139 r_lrange_other 4.753 r_dihedral_angle_2_deg 3.368 r_scangle_it 2.85 r_scangle_other 2.849 r_mcangle_other 1.83 r_mcangle_it 1.825
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.809 r_dihedral_angle_3_deg 12.024 r_dihedral_angle_1_deg 7.05 r_lrange_it 5.139 r_lrange_other 4.753 r_dihedral_angle_2_deg 3.368 r_scangle_it 2.85 r_scangle_other 2.849 r_mcangle_other 1.83 r_mcangle_it 1.825 r_scbond_it 1.781 r_scbond_other 1.781 r_angle_refined_deg 1.52 r_mcbond_it 1.134 r_mcbond_other 1.129 r_angle_other_deg 0.505 r_nbd_refined 0.214 r_symmetry_nbd_refined 0.21 r_nbd_other 0.205 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.171 r_metal_ion_refined 0.165 r_symmetry_xyhbond_nbd_refined 0.162 r_xyhbond_nbd_refined 0.157 r_symmetry_xyhbond_nbd_other 0.096 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.069 r_xyhbond_nbd_other 0.032 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3640 Nucleic Acid Atoms Solvent Atoms 810 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing