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Crystal structure of bromoperoxidase from Bacillus anthracis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BRO PDB entry 1BRO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 0.2 M Magnesium chloride, 0.1 M Hepes buffer, 25% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.02 39.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.037 α = 90 b = 48.326 β = 94.05 c = 101.932 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 SBC-3 2008-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9792 APS 19-BM
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 1.74 28.4 99.7 0.077 27.405 6.8 76114 76114 30.7
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 1.74 1.78 99.8 0.651 2.56 6.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1BRO 1.74 27.5 75908 75908 3809 98.92 0.16524 0.16362 0.1738 0.19484 0.2045 RANDOM 17.094
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] -0.09 0.61 0.37 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.053 r_dihedral_angle_3_deg 15.673 r_dihedral_angle_4_deg 14.598 r_dihedral_angle_1_deg 5.888 r_scangle_it 4.192 r_scbond_it 2.71 r_angle_refined_deg 1.68 r_mcangle_it 1.607 r_angle_other_deg 0.977 r_mcbond_it 0.965
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.053 r_dihedral_angle_3_deg 15.673 r_dihedral_angle_4_deg 14.598 r_dihedral_angle_1_deg 5.888 r_scangle_it 4.192 r_scbond_it 2.71 r_angle_refined_deg 1.68 r_mcangle_it 1.607 r_angle_other_deg 0.977 r_mcbond_it 0.965 r_mcbond_other 0.338 r_chiral_restr 0.108 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6524 Nucleic Acid Atoms Solvent Atoms 723 Heterogen Atoms 5
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction MOLREP phasing HKL-3000 phasing