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Characterization of the Inhibitor Binding Site of the Dehaloperoxidase-Hemoglobin from Amphitrite ornata using High-Pressure Xenon Derivatization
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QFK PDB ENTRY 2QFK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.9 277 0.2 M ammonium sulfate, 32% PEG 4000, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.16 42.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.945 α = 90 b = 67.708 β = 90 c = 68.359 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 IMAGE PLATE RIGAKU RAXIS IV 2009-05-06 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) 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 1.71 30.51 97.37 0.063 15.3 3.3 28155 27415 2
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) 1.71 1.755 90.05 0.241 2.8 1.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2QFK 1.711 30.51 27415 1473 97.37 0.19773 0.19598 0.22959 0.2295 RANDOM 13.833
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] 0.16 -0.34 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.358 r_dihedral_angle_4_deg 16.83 r_dihedral_angle_3_deg 15.668 r_dihedral_angle_1_deg 3.938 r_scangle_it 1.83 r_scbond_it 1.133 r_angle_refined_deg 0.987 r_mcangle_it 0.716 r_mcbond_it 0.38 r_chiral_restr 0.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.358 r_dihedral_angle_4_deg 16.83 r_dihedral_angle_3_deg 15.668 r_dihedral_angle_1_deg 3.938 r_scangle_it 1.83 r_scbond_it 1.133 r_angle_refined_deg 0.987 r_mcangle_it 0.716 r_mcbond_it 0.38 r_chiral_restr 0.079 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2182 Nucleic Acid Atoms Solvent Atoms 276 Heterogen Atoms 110
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling