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Crystal structure of Vanadium-dependent haloperoxidase R425D mutant (A. marina)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LPC Crystal structure of Vanadium-dependent Haloperoxidase from A. marina
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.1 M TRIS, 1.25 M Ammoniumdihydrogenphosphate, 0.5 mM potassium vanadate
Crystal Properties Matthews coefficient Solvent content 4.18 70.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 308.38 α = 90 b = 308.38 β = 90 c = 308.38 γ = 90
Symmetry Space Group F 41 3 2
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 X 16M 2019-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 3.5 30 96.5 0.122 9.4 5 15830
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 3.5 3.6 96.6 0.632 5
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3.5 30 15012 790 96.34 0.2253 0.2243 0.2443 0.2306 RANDOM 96.498
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 29.969 r_dihedral_angle_3_deg 15.103 r_dihedral_angle_4_deg 12.785 r_dihedral_angle_1_deg 4.875 r_angle_refined_deg 1.214 r_angle_other_deg 1.052 r_rigid_bond_restr 0.072 r_chiral_restr 0.037 r_bond_refined_d 0.002 r_gen_planes_refined 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.969 r_dihedral_angle_3_deg 15.103 r_dihedral_angle_4_deg 12.785 r_dihedral_angle_1_deg 4.875 r_angle_refined_deg 1.214 r_angle_other_deg 1.052 r_rigid_bond_restr 0.072 r_chiral_restr 0.037 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4876 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling REFMAC phasing