☰ Navigation Tabs
Multicopper oxidase from Campylobacter jejuni: a metallo-oxidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YXW PDB ENTRY 2YXW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 32% PEG 3350, 0.2M MGCL2, 0.1M BIS-TRIS PROPANE PH5.5, 3% DIOXANE.
Crystal Properties Matthews coefficient Solvent content 1.94 36.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.81 α = 90 b = 94.86 β = 100.63 c = 50.38 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 CCD ADSC QUANTUM 315r 2009-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.95 49.51 99.4 0.07 14.9 4.3 32673 2 33.62
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 1.95 2.06 97.3 0.37 3.5 4.2
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 2YXW 1.95 49.51 30986 1656 99.35 0.16255 0.1602 0.1592 0.20714 0.2058 RANDOM 26.754
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] 0.11 0.7 -0.16 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.557 r_dihedral_angle_4_deg 17.452 r_dihedral_angle_3_deg 15.862 r_dihedral_angle_1_deg 7.055 r_scangle_it 4.031 r_scbond_it 2.488 r_angle_refined_deg 1.534 r_mcangle_it 1.447 r_mcbond_it 0.811 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.557 r_dihedral_angle_4_deg 17.452 r_dihedral_angle_3_deg 15.862 r_dihedral_angle_1_deg 7.055 r_scangle_it 4.031 r_scbond_it 2.488 r_angle_refined_deg 1.534 r_mcangle_it 1.447 r_mcbond_it 0.811 r_nbtor_refined 0.313 r_symmetry_hbond_refined 0.204 r_nbd_refined 0.197 r_xyhbond_nbd_refined 0.144 r_symmetry_vdw_refined 0.142 r_chiral_restr 0.11 r_metal_ion_refined 0.038 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other 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 3820 Nucleic Acid Atoms Solvent Atoms 318 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MrBUMP phasing