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Three-dimensional structure of the K109A mutant of Paracoccus pantotrophus pseudoazurin at pH 5.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ERX PDB ENTRY 3ERX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 3.0 - 3.2 M AMMONIUM SULPHATE, 50 MM POTASSIUM PHOSPHATE AT PH 5.5
Crystal Properties Matthews coefficient Solvent content 2.12 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.85 α = 90 b = 66.17 β = 90 c = 68.63 γ = 90
Symmetry Space Group P 2 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 CCD ADSC QUANTUM 4 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.76 29.8 100 0.08 23.3 13.9 23180 23.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.76 1.8 100 0.4 6.1 12.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3ERX 1.76 29.82 21956 1186 99.96 0.15185 0.14897 0.1717 0.20743 0.1676 RANDOM 18.081
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] -0.42 0.62 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.466 r_dihedral_angle_3_deg 15.496 r_dihedral_angle_4_deg 11.909 r_long_range_B_refined 11.207 r_long_range_B_other 10.904 r_dihedral_angle_1_deg 6.495 r_angle_refined_deg 2.07 r_scangle_other 1.649 r_scbond_it 1.398 r_scbond_other 1.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.466 r_dihedral_angle_3_deg 15.496 r_dihedral_angle_4_deg 11.909 r_long_range_B_refined 11.207 r_long_range_B_other 10.904 r_dihedral_angle_1_deg 6.495 r_angle_refined_deg 2.07 r_scangle_other 1.649 r_scbond_it 1.398 r_scbond_other 1.071 r_mcangle_it 0.992 r_mcangle_other 0.991 r_angle_other_deg 0.929 r_mcbond_other 0.592 r_mcbond_it 0.591 r_chiral_restr 0.113 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 1857 Nucleic Acid Atoms Solvent Atoms 410 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing