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X-ray Crystal Structure of Pseudoazurin Met16His Variant at pH 4.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 298 31% PEG1500, 0.1 M potassium phosphate (pH 4.0)
Crystal Properties Matthews coefficient Solvent content 2.15 42.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.196 α = 90 b = 60.476 β = 105.81 c = 54.865 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 2022-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.052 Photon Factory BL-1A
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 1.36 39.77 99.3 0.042 0.058 0.039 0.997 13.6 3.3 47237
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 1.36 1.38 0.267 0.365 0.247 0.884 3
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 4YL4 1.36 39.77 47216 2207 99.245 0.129 0.1279 0.1377 0.1603 0.1634 15.552
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] 0.172 1.725 -2.427 1.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.084 r_dihedral_angle_3_deg 14.383 r_dihedral_angle_1_deg 6.948 r_dihedral_angle_2_deg 6.637 r_rigid_bond_restr 5.014 r_lrange_it 3.639 r_lrange_other 2.92 r_scangle_it 1.859 r_scangle_other 1.858 r_angle_refined_deg 1.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.084 r_dihedral_angle_3_deg 14.383 r_dihedral_angle_1_deg 6.948 r_dihedral_angle_2_deg 6.637 r_rigid_bond_restr 5.014 r_lrange_it 3.639 r_lrange_other 2.92 r_scangle_it 1.859 r_scangle_other 1.858 r_angle_refined_deg 1.65 r_mcangle_it 1.613 r_mcangle_other 1.613 r_scbond_other 1.459 r_scbond_it 1.458 r_mcbond_it 1.261 r_mcbond_other 1.261 r_angle_other_deg 0.542 r_symmetry_nbd_refined 0.343 r_nbd_other 0.243 r_nbd_refined 0.217 r_xyhbond_nbd_refined 0.216 r_symmetry_nbd_other 0.197 r_symmetry_xyhbond_nbd_refined 0.191 r_nbtor_refined 0.173 r_metal_ion_refined 0.129 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.086 r_bond_refined_d 0.01 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 1830 Nucleic Acid Atoms Solvent Atoms 403 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing