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Structure of the H55D mutant of dehaloperoxidase-hemoglobin A from Amphitrite ornata
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 6.5 277 0.2 M Ammonuim Sulfate, 34% w/v PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.11 41.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.955 α = 90 b = 67.917 β = 90 c = 67.905 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 CCD MARMOSAIC 225 mm CCD 2010-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 0.91339 APS 22-BM
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 1.52 48.02 97.7521 0.134 5.68 2.8 39120 38241 2 5.8
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 1.52 1.61 97.3 0.438 2.56 2.8 6615
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 1.52 35 39120 38241 2114 97.75 0.22486 0.22317 0.1878 0.25523 0.219 RANDOM 5.87
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] 0.7 -0.01 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.61 r_dihedral_angle_4_deg 16.341 r_dihedral_angle_3_deg 15.65 r_dihedral_angle_1_deg 4.218 r_scangle_it 1.489 r_angle_refined_deg 0.999 r_scbond_it 0.962 r_mcangle_it 0.585 r_mcbond_it 0.311 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.61 r_dihedral_angle_4_deg 16.341 r_dihedral_angle_3_deg 15.65 r_dihedral_angle_1_deg 4.218 r_scangle_it 1.489 r_angle_refined_deg 0.999 r_scbond_it 0.962 r_mcangle_it 0.585 r_mcbond_it 0.311 r_chiral_restr 0.083 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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 2178 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 101
Software Software Software Name Purpose HKL-2000 data collection PHASES phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling