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Vanadium-dependent bromoperoxidase from Corallina pilulifera in complex with chloride
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UP8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.1M Tris-HBr, pH 7.4, 1.3M ammonium dihydrogen phosphate
Crystal Properties Matthews coefficient Solvent content 3.25 62.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.115 α = 90 b = 182.115 β = 90 c = 177.602 γ = 120
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 MAR CCD 165 mm 2002-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 0.84820 EMBL/DESY, HAMBURG BW7A
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 1.999 99 97.4 0.063 11.2 3.3 218890
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 1.999 2.07 0.219 2.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1up8 1.999 19.962 211873 10625 94.254 0.148 0.146 0.146 0.1928 0.1928 24.081
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] 0.283 0.141 0.283 -0.918
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.345 r_dihedral_angle_4_deg 17.029 r_dihedral_angle_3_deg 13.298 r_scangle_it 9.257 r_lrange_it 9.081 r_scbond_it 8.651 r_dihedral_angle_1_deg 6.193 r_mcangle_it 5.558 r_mcbond_it 5.313 r_angle_refined_deg 1.772
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.345 r_dihedral_angle_4_deg 17.029 r_dihedral_angle_3_deg 13.298 r_scangle_it 9.257 r_lrange_it 9.081 r_scbond_it 8.651 r_dihedral_angle_1_deg 6.193 r_mcangle_it 5.558 r_mcbond_it 5.313 r_angle_refined_deg 1.772 r_nbtor_refined 0.323 r_metal_ion_refined 0.29 r_symmetry_nbd_refined 0.237 r_nbd_refined 0.215 r_symmetry_xyhbond_nbd_refined 0.186 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.118 r_ncsr_local_group_4 0.055 r_ncsr_local_group_2 0.054 r_ncsr_local_group_6 0.054 r_ncsr_local_group_1 0.053 r_ncsr_local_group_3 0.049 r_ncsr_local_group_5 0.049 r_bond_refined_d 0.013 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18420 Nucleic Acid Atoms Solvent Atoms 3214 Heterogen Atoms 460
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing