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Dehaloperoxidase B in complex with substrate o-cresol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IXF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 MPEG 2000, ammonium sulphate, sodium cacodylate
Crystal Properties Matthews coefficient Solvent content 2.2 44.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.273 α = 90 b = 67.69 β = 90 c = 67.68 γ = 90
Symmetry Space Group P 21 21 21
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 RAYONIX MX300-HS 2019-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.00 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 1.6 37.26 98.44 0.054 0.025 0.997 28.6 3.9 34115 2 16.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.643 85.97 0.594 0.36 0.721 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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3ixf 1.602 37.26 35955 1840 98.445 0.172 0.171 0.1821 0.1986 0.2084 18.364
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] 1.346 -0.692 -0.654
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.215 r_dihedral_angle_4_deg 19.477 r_dihedral_angle_3_deg 14.331 r_dihedral_angle_1_deg 5.45 r_lrange_it 5.204 r_lrange_other 5.17 r_angle_refined_deg 1.53 r_angle_other_deg 1.502 r_scangle_it 1.144 r_scangle_other 1.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.215 r_dihedral_angle_4_deg 19.477 r_dihedral_angle_3_deg 14.331 r_dihedral_angle_1_deg 5.45 r_lrange_it 5.204 r_lrange_other 5.17 r_angle_refined_deg 1.53 r_angle_other_deg 1.502 r_scangle_it 1.144 r_scangle_other 1.126 r_mcangle_it 0.792 r_mcangle_other 0.792 r_scbond_it 0.782 r_scbond_other 0.762 r_mcbond_it 0.455 r_mcbond_other 0.453 r_nbd_refined 0.258 r_symmetry_nbd_other 0.187 r_nbd_other 0.184 r_nbtor_refined 0.179 r_symmetry_nbd_refined 0.173 r_xyhbond_nbd_refined 0.155 r_symmetry_xyhbond_nbd_refined 0.119 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.077 r_symmetry_xyhbond_nbd_other 0.019 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.006 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2142 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms 156
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing