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Crystal structure of human heme oxygenase-2 C127A (HO-2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N45 PDB entry 1N45
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 Protein solution (5 mg/ml Protein, 0.050 M Potassium chloride, 0.005 M Tris-HCl pH 8.5) mixed in a 1.5:1 ratio with the well solution (40% PEG 1500, 0.20 M Potassium glutamate, 0.10 M Triethanolamine, pH 8.5). Cryoprotected with well solution, VAPOR DIFUSSION, HANGING DROP, temperature 277K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.6 52.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.769 α = 90 b = 86.017 β = 90 c = 97.753 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 focusing mirrors in K-B geometry 2007-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97933 APS 23-ID-D
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 2.3 49.148 95.9 0.082 13.505 7.3 28128
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 2.3 2.38 78.2 0.608 1.929 3.9 2245
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1N45 2.4 49.148 25217 1275 98.431 0.204 0.201 0.1991 0.253 0.2519 RANDOM 59.622
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] -2.315 -1.049 3.364
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.67 r_dihedral_angle_4_deg 22.585 r_dihedral_angle_3_deg 16.946 r_dihedral_angle_1_deg 5.145 r_scangle_it 1.966 r_angle_refined_deg 1.255 r_scbond_it 1.232 r_mcangle_it 0.799 r_mcbond_it 0.514 r_nbtor_refined 0.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.67 r_dihedral_angle_4_deg 22.585 r_dihedral_angle_3_deg 16.946 r_dihedral_angle_1_deg 5.145 r_scangle_it 1.966 r_angle_refined_deg 1.255 r_scbond_it 1.232 r_mcangle_it 0.799 r_mcbond_it 0.514 r_nbtor_refined 0.294 r_symmetry_hbond_refined 0.286 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.155 r_symmetry_vdw_refined 0.103 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3538 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 70
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