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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 Ammonuim Sulfate, 32% w/v PEG 4000, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.16 42.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.56 α = 90 b = 67.423 β = 90 c = 67.96 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 2009-11-24 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 1.72 47.86 99.87 0.103 18.4 6.3 27775 27739 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) 1.72 1.765 100 0.773 2.5 6.2
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 1.72 47.86 27775 27739 1465 99.87 0.18619 0.18342 0.1798 0.2408 0.238 RANDOM 17.708
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] 0.52 -0.39 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.382 r_dihedral_angle_4_deg 17.618 r_dihedral_angle_3_deg 16.93 r_dihedral_angle_1_deg 4.125 r_scangle_it 2.557 r_scbond_it 1.604 r_angle_refined_deg 1.168 r_mcangle_it 0.891 r_mcbond_it 0.485 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.382 r_dihedral_angle_4_deg 17.618 r_dihedral_angle_3_deg 16.93 r_dihedral_angle_1_deg 4.125 r_scangle_it 2.557 r_scbond_it 1.604 r_angle_refined_deg 1.168 r_mcangle_it 0.891 r_mcbond_it 0.485 r_chiral_restr 0.086 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 2184 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 105
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling