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Crystal structure of Dehaloperoxidase B in complex with substrate cyclohexene
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 277 MPEG 2000, ammonium sulfate, sodium cacodylate
Crystal Properties Matthews coefficient Solvent content 2.2 43.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.092 α = 90 b = 67.684 β = 90 c = 67.684 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 PIXEL DECTRIS EIGER R 4M 2023-08-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2 17.34 99.47 0.999 16 6.2 18829
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 2 2.051 0.705
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2 17.339 18829 929 99.466 0.198 0.1946 0.203 0.251 0.2603 38.438
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] 1.496 -1.135 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.296 r_dihedral_angle_6_deg 14.569 r_lrange_it 8.549 r_lrange_other 8.525 r_dihedral_angle_2_deg 6.995 r_scangle_it 6.422 r_scangle_other 6.414 r_dihedral_angle_1_deg 6.22 r_mcangle_it 4.624 r_mcangle_other 4.623
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.296 r_dihedral_angle_6_deg 14.569 r_lrange_it 8.549 r_lrange_other 8.525 r_dihedral_angle_2_deg 6.995 r_scangle_it 6.422 r_scangle_other 6.414 r_dihedral_angle_1_deg 6.22 r_mcangle_it 4.624 r_mcangle_other 4.623 r_scbond_it 4.434 r_scbond_other 4.411 r_mcbond_it 3.284 r_mcbond_other 3.284 r_angle_refined_deg 1.553 r_angle_other_deg 0.549 r_nbd_refined 0.268 r_symmetry_nbd_other 0.209 r_nbtor_refined 0.199 r_symmetry_xyhbond_nbd_refined 0.188 r_xyhbond_nbd_refined 0.184 r_nbd_other 0.177 r_symmetry_nbd_refined 0.15 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.07 r_symmetry_xyhbond_nbd_other 0.043 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2162 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 152
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling PHASER phasing