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Crystal structure of heme oxygenase from Corynebacterium diphtheriae (HmuO) in complex with hydroxyheme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V8X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 303 ammonium sulfate, NaI, MES, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 303K
Crystal Properties Matthews coefficient Solvent content 2.47 50.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.943 α = 90 b = 62.761 β = 100.96 c = 107.813 γ = 90
Symmetry Space Group P 1 21 1
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 ADSC QUANTUM 210r 2006-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.6 50 99.7 1 30.37 3.8 93101 20.83
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 0.878
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.6 30.76 1.36 92993 4758 99.55 0.1721 0.1703 0.1715 0.2072 0.2081 28.53
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.0856 f_angle_d 1.6318 f_chiral_restr 0.0848 f_bond_d 0.0166 f_plane_restr 0.0146
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4943 Nucleic Acid Atoms Solvent Atoms 687 Heterogen Atoms 185
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction Aimless data scaling REFMAC phasing