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Three-dimensional structure of Paracoccus pantotrophus pseudoazurin at pH 6.5
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 6.5 3.0 - 3.2 M AMMONIUM SULPHATE, 50 MM POTASSIUM PHOSPHATE PH 6.5
Crystal Properties Matthews coefficient Solvent content 3.16 62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.28 α = 90 b = 57.87 β = 125.99 c = 67.1 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 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 27.85 98.5 0.06 11.8 3.4 32561 11.8
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 97.4 0.16 5.1 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 PDB ENTRY 3ERX 1.76 27.85 30907 1653 98.33 0.16801 0.1659 0.20631 0.222 RANDOM 14.227
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] -0.01 -0.34 0.43 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.543 r_dihedral_angle_3_deg 13.31 r_dihedral_angle_1_deg 6.761 r_dihedral_angle_4_deg 6.599 r_angle_refined_deg 2.155 r_scbond_it 1.853 r_mcangle_it 1.146 r_angle_other_deg 0.927 r_mcbond_it 0.72 r_mcbond_other 0.717
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.543 r_dihedral_angle_3_deg 13.31 r_dihedral_angle_1_deg 6.761 r_dihedral_angle_4_deg 6.599 r_angle_refined_deg 2.155 r_scbond_it 1.853 r_mcangle_it 1.146 r_angle_other_deg 0.927 r_mcbond_it 0.72 r_mcbond_other 0.717 r_chiral_restr 0.119 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1865 Nucleic Acid Atoms Solvent Atoms 438 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing