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X-ray Crystal Structure of Pseudoazurin Met16Gly Variant, Reduced Form.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BQK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 30 % PEG1000, 0.1 M Tris-HCl
Crystal Properties Matthews coefficient Solvent content 3.17 61.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.53 α = 90 b = 91.49 β = 90.04 c = 78.57 γ = 90
Symmetry Space Group C 1 2 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 IMAGE PLATE RIGAKU RAXIS VII 2017-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2 30.002 100 0.055 0.065 0.034 15.2 3.6 43773
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 100 0.352 0.352 0.417 0.22 2.2 3.5
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1BQK 2 29.92 41565 2191 99.92 0.17369 0.17209 0.20254 0.1884 RANDOM 31.023
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.489 r_dihedral_angle_3_deg 16.675 r_dihedral_angle_4_deg 12.16 r_long_range_B_refined 8.722 r_long_range_B_other 8.535 r_dihedral_angle_1_deg 6.888 r_scangle_other 6.361 r_scbond_it 4.206 r_scbond_other 4.204 r_mcangle_other 3.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.489 r_dihedral_angle_3_deg 16.675 r_dihedral_angle_4_deg 12.16 r_long_range_B_refined 8.722 r_long_range_B_other 8.535 r_dihedral_angle_1_deg 6.888 r_scangle_other 6.361 r_scbond_it 4.206 r_scbond_other 4.204 r_mcangle_other 3.97 r_mcangle_it 3.969 r_mcbond_it 2.989 r_mcbond_other 2.984 r_angle_refined_deg 1.961 r_angle_other_deg 1.067 r_chiral_restr 0.127 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3531 Nucleic Acid Atoms Solvent Atoms 415 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement SCALA data scaling MOLREP phasing PDB_EXTRACT data extraction Coot model building CrystalClear data collection iMOSFLM data reduction