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Vanadate complex of the vanadium-dependent bromoperoxidase from Corallina pilulifera
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 293 50 mM Tris-H2SO4, pH 6.8, 0.4M KBr, 1mM Na3VO4, 20% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.54 51.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 199.601 α = 90 b = 199.601 β = 90 c = 199.601 γ = 90
Symmetry Space Group P 21 3
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 2003-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 0.9200 EMBL/DESY, HAMBURG BW7A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.15 14.965 96.4 0.155 0.977 8.1 4.9 142571
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.19 0.502 0.809
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 2.15 14.965 141462 7104 98.889 0.147 0.1443 0.1443 0.1945 0.1945 19.248
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.498 r_dihedral_angle_4_deg 17.836 r_dihedral_angle_3_deg 13.457 r_lrange_it 6.985 r_scangle_it 6.469 r_dihedral_angle_1_deg 6.081 r_scbond_it 5.582 r_mcangle_it 3.809 r_mcbond_it 3.248 r_angle_refined_deg 1.333
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.498 r_dihedral_angle_4_deg 17.836 r_dihedral_angle_3_deg 13.457 r_lrange_it 6.985 r_scangle_it 6.469 r_dihedral_angle_1_deg 6.081 r_scbond_it 5.582 r_mcangle_it 3.809 r_mcbond_it 3.248 r_angle_refined_deg 1.333 r_nbtor_refined 0.312 r_symmetry_nbd_refined 0.238 r_nbd_refined 0.208 r_symmetry_xyhbond_nbd_refined 0.143 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.091 r_metal_ion_refined 0.085 r_ncsr_local_group_1 0.054 r_ncsr_local_group_4 0.053 r_ncsr_local_group_3 0.052 r_ncsr_local_group_6 0.052 r_ncsr_local_group_5 0.05 r_ncsr_local_group_2 0.044 r_bond_refined_d 0.007 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18448 Nucleic Acid Atoms Solvent Atoms 2952 Heterogen Atoms 365
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing O model building Coot model building