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Ensemble refinement of the protein crystal structure of human heme oxygenase-2 C127A (HO-2) with bound heme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QPP PDB entry 2QPP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 Protein solution (5 mg/ml Protein, 1:1 ratio Heme, 2% DMSO, 0.050 M Potassium chloride, 0.050 M Tris-HCl pH 7.5) mixed in a 1.5:1 ratio with the Well solution (33% PEG DME 500, 0.020 M Magnesium chloride, 0.10 M HEPES pH 7.5). Cryoprotected with well solution, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.56 51.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.977 α = 90 b = 85.094 β = 90 c = 97.846 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 300 mm CCD Adjustable focus K-B pair Si plus Pt, Rh coatings 2007-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.97946 APS 23-ID-B
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 2.32 42.413 85.6 0.083 16.268 11.6 24030
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 2.32 2.4 27.4 0.715 0.776 1.8 752
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION Multi-conformer re-refinement THROUGHOUT PDB entry 2QPP 2.61 39.02 19515 1005 99.3 0.161 0.2092 0.249 0.2799 RANDOM 56.5
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 c_dihedral_angle_d 20.1 c_scangle_it 2.2 c_scbond_it 1.66 c_angle_deg 1.6 c_mcangle_it 1.56 c_mcbond_it 1.02 c_improper_angle_d 0.95 c_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3552 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 86
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing