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Dehaloperoxidase B from Amphitrite ornata: benzotriazole complex
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 6.4 277 12 mg/ml DHP B in 20 mM Na cacodylate (pH 6.4) was mixed with a reservoir solution comprising 14-20% (w/v) PEG 4000 and 150-250 mM ammonium sulfate.
Crystal Properties Matthews coefficient Solvent content 2.28 45.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.68 α = 90 b = 67.07 β = 90 c = 69.01 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 PILATUS 2M 2015-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.14 45.6 98 0.037 1 17.6 4 100913
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.14 1.17 95.3 0.801 0.571 1.4 3.2
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 (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 3ixf 1.14 45.57 95874 4962 97.79 0.1453 0.1436 0.1426 0.1794 0.1783 RANDOM 18.354
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] -0.24 -0.12 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.667 r_sphericity_free 25.724 r_dihedral_angle_4_deg 22.108 r_dihedral_angle_3_deg 12.392 r_sphericity_bonded 11.036 r_dihedral_angle_1_deg 5.062 r_rigid_bond_restr 3.466 r_mcangle_it 2.264 r_angle_refined_deg 1.967 r_mcbond_it 1.783
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.667 r_sphericity_free 25.724 r_dihedral_angle_4_deg 22.108 r_dihedral_angle_3_deg 12.392 r_sphericity_bonded 11.036 r_dihedral_angle_1_deg 5.062 r_rigid_bond_restr 3.466 r_mcangle_it 2.264 r_angle_refined_deg 1.967 r_mcbond_it 1.783 r_mcbond_other 1.777 r_angle_other_deg 1.685 r_chiral_restr 0.143 r_bond_refined_d 0.019 r_gen_planes_other 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2162 Nucleic Acid Atoms Solvent Atoms 402 Heterogen Atoms 120
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing