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X-ray Crystal Structure of Pseudoazurin Met16Gly variant (Tris-HCl pH 7.6)
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, 39% (w/v) PEG 1500
Crystal Properties Matthews coefficient Solvent content 1.93 36.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.748 α = 90 b = 69.984 β = 90 c = 94.239 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 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 1.5 47.12 100 0.998 11.2 6.7 65079 5.985
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 1.5 1.53 100 0.661 2 6.7
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 1.5 47.12 65010 3261 99.935 0.143 0.1401 0.1388 0.198 0.1954 11.808
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] -0.082 -0.112 0.194
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.312 r_lrange_it 14.067 r_dihedral_angle_2_deg 13.695 r_lrange_other 10.78 r_dihedral_angle_3_deg 10.465 r_dihedral_angle_1_deg 7.113 r_scangle_it 4.899 r_scangle_other 4.898 r_mcangle_other 4.046 r_mcangle_it 4.044
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.312 r_lrange_it 14.067 r_dihedral_angle_2_deg 13.695 r_lrange_other 10.78 r_dihedral_angle_3_deg 10.465 r_dihedral_angle_1_deg 7.113 r_scangle_it 4.899 r_scangle_other 4.898 r_mcangle_other 4.046 r_mcangle_it 4.044 r_rigid_bond_restr 3.252 r_scbond_it 3.214 r_scbond_other 3.214 r_mcbond_it 2.567 r_mcbond_other 2.564 r_angle_refined_deg 1.611 r_angle_other_deg 0.552 r_symmetry_nbd_refined 0.274 r_nbd_other 0.219 r_nbd_refined 0.218 r_symmetry_nbd_other 0.201 r_nbtor_refined 0.173 r_metal_ion_refined 0.157 r_xyhbond_nbd_refined 0.148 r_symmetry_xyhbond_nbd_refined 0.133 r_chiral_restr 0.083 r_symmetry_nbtor_other 0.083 r_symmetry_xyhbond_nbd_other 0.02 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3590 Nucleic Acid Atoms Solvent Atoms 809 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction XDS data scaling MOLREP phasing