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R396W mutant 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 0.1 M Tris-HCl and 2 M ammonium dihydrogen phosphate at pH 5.0
Crystal Properties Matthews coefficient Solvent content 3.24 62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.148 α = 90 b = 182.148 β = 90 c = 177.186 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 2003-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B 0.9076 EMBL/DESY, HAMBURG BW7B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.92 49.603 97.8 0.997 16.5 5.6 246831
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.92 1.95 80.9 0.38 3
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 1.922 49.603 244950 2460 96.98 0.1531 0.1531 0.1531 0.1855 0.1854 30.913
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] 0.549 0.275 0.549 -1.781
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.54 r_dihedral_angle_4_deg 16.917 r_dihedral_angle_3_deg 13.916 r_lrange_it 8.253 r_scangle_it 8.248 r_scbond_it 8.019 r_dihedral_angle_1_deg 6.134 r_mcangle_it 5.292 r_mcbond_it 4.904 r_angle_refined_deg 1.556
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.54 r_dihedral_angle_4_deg 16.917 r_dihedral_angle_3_deg 13.916 r_lrange_it 8.253 r_scangle_it 8.248 r_scbond_it 8.019 r_dihedral_angle_1_deg 6.134 r_mcangle_it 5.292 r_mcbond_it 4.904 r_angle_refined_deg 1.556 r_nbtor_refined 0.322 r_symmetry_nbd_refined 0.271 r_nbd_refined 0.219 r_symmetry_xyhbond_nbd_refined 0.16 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.102 r_ncsr_local_group_6 0.061 r_ncsr_local_group_2 0.06 r_ncsr_local_group_4 0.06 r_ncsr_local_group_1 0.058 r_ncsr_local_group_3 0.057 r_ncsr_local_group_5 0.054 r_bond_refined_d 0.01 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18440 Nucleic Acid Atoms Solvent Atoms 3147 Heterogen Atoms 444
Software Software Software Name Purpose REFMAC refinement DENZO data reduction XDS data reduction SCALEPACK data scaling XSCALE data scaling MOLREP phasing O model building Coot model building