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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 2Q32 PDB entry 2Q32
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 2.6 51.6
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-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2Q32 2.61 40.962 19515 1005 99.364 0.205 0.202 0.256 0.2993 RANDOM 65.958
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] -0.34 -1.216 1.555
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.971 r_dihedral_angle_4_deg 19.242 r_dihedral_angle_3_deg 15.542 r_dihedral_angle_1_deg 4.47 r_mcangle_it 1.234 r_scangle_it 1.167 r_angle_refined_deg 0.951 r_scbond_it 0.859 r_mcbond_it 0.732 r_nbtor_refined 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.971 r_dihedral_angle_4_deg 19.242 r_dihedral_angle_3_deg 15.542 r_dihedral_angle_1_deg 4.47 r_mcangle_it 1.234 r_scangle_it 1.167 r_angle_refined_deg 0.951 r_scbond_it 0.859 r_mcbond_it 0.732 r_nbtor_refined 0.29 r_symmetry_hbond_refined 0.266 r_nbd_refined 0.182 r_symmetry_vdw_refined 0.152 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.07 r_bond_refined_d 0.006 r_gen_planes_refined 0.003
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 DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling