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Crystal structure of multi-copper oxidase from Pseudomonas Parafulva
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VOW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 288 Crystallized in plastic sitting drop trays, 30 nl of protein (concentration 10 mg/mL) combined with 30 nl precipitant:
0.0425 M BICINE pH 9.0
0.0425 M Sodium chloride
8.5% v/v Polyethylene glycol monomethyl ether 550
7.5% v/v Glycerol
Solution was equilibrated against a reservoir of 60% PEG 3350.
Crystal Properties Matthews coefficient Solvent content 5.8 78.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 170.35 α = 90 b = 170.35 β = 90 c = 131 γ = 120
Symmetry Space Group P 62 2 2
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 EIGER2 X 9M 2018-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.9202 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.8 50 92.3 0.29 0.997 8.38 29.33 10690
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.8 3.9 2.578 0.258
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 6VOW 3.8 30 10435 215 92.35 0.25802 0.2577 0.2674 0.27404 0.2847 RANDOM 195.234
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] 0.23 0.11 0.23 -0.74
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 40.449 r_long_range_B_refined 40.447 r_dihedral_angle_2_deg 38.621 r_mcangle_it 27.386 r_mcangle_other 27.379 r_scangle_other 24.129 r_dihedral_angle_3_deg 22.836 r_dihedral_angle_4_deg 17.043 r_mcbond_other 16.926 r_mcbond_it 16.925
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 40.449 r_long_range_B_refined 40.447 r_dihedral_angle_2_deg 38.621 r_mcangle_it 27.386 r_mcangle_other 27.379 r_scangle_other 24.129 r_dihedral_angle_3_deg 22.836 r_dihedral_angle_4_deg 17.043 r_mcbond_other 16.926 r_mcbond_it 16.925 r_scbond_it 14.191 r_scbond_other 14.148 r_dihedral_angle_1_deg 12.096 r_angle_refined_deg 1.984 r_angle_other_deg 1.202 r_chiral_restr 0.108 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.003 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 3198 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing