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Mutation of Methionine-86 in Dehaloperoxidase-hemoglobin: Effects of the Asp-His-Fe Triad in a 3/3 Globin
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, 36% w/v PEG 4000, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.23 44.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.364 α = 90 b = 67.496 β = 90 c = 68.039 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 MAR scanner 345 mm plate Osmic Confocal X-ray optics 2010-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 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 2.194 35 96.41 0.138 5.8 7 14062 13557 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) 2.194 2.25 70.9 0.369 2.9 7.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 2QFK 2.194 35 14062 13557 686 96.41 0.23332 0.23025 0.2016 0.29696 0.2355 RANDOM 18.79
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] 25 -13.78 -11.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.155 r_dihedral_angle_4_deg 18.141 r_dihedral_angle_3_deg 18.044 r_dihedral_angle_1_deg 4.849 r_scangle_it 1.761 r_angle_refined_deg 1.185 r_scbond_it 1.099 r_mcangle_it 0.635 r_mcbond_it 0.337 r_chiral_restr 0.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.155 r_dihedral_angle_4_deg 18.141 r_dihedral_angle_3_deg 18.044 r_dihedral_angle_1_deg 4.849 r_scangle_it 1.761 r_angle_refined_deg 1.185 r_scbond_it 1.099 r_mcangle_it 0.635 r_mcbond_it 0.337 r_chiral_restr 0.091 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 195 Heterogen Atoms 105
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling