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Crystal Structure of Human Heme Oxygenase-1 in Complex with 1-(Adamantan-1-yl)-2-(1H-imidazol-1-yl)ethanone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N3U PDB Entry 1N3U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 2.16M ammonium sulfate, 0.9% 1,6-hexanediol, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.89 34.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52 α = 90 b = 52.446 β = 90 c = 74.488 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 270 Horizontal bent Si(111), asymmetrically cut with water cooled Cu Block. Rh-coated Si mirror for vertical focusing. 2007-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.918 CHESS F1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.54 50 97.1 0.086 0.086 36.5 6.5 57555 55840 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.54 1.6 82.8 0.356 0.356 4.4 3.7 4836
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 1N3U 1.54 50 54625 54625 2899 96.85 0.19544 0.19377 0.1915 0.22633 0.2241 RANDOM 15.609
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] 0.3 0.07 -0.46 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.735 r_dihedral_angle_4_deg 19.006 r_dihedral_angle_3_deg 14.094 r_dihedral_angle_1_deg 4.516 r_scangle_it 3.596 r_scbond_it 2.326 r_mcangle_it 1.341 r_angle_refined_deg 1.217 r_mcbond_it 0.865 r_xyhbond_nbd_refined 0.348
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.735 r_dihedral_angle_4_deg 19.006 r_dihedral_angle_3_deg 14.094 r_dihedral_angle_1_deg 4.516 r_scangle_it 3.596 r_scbond_it 2.326 r_mcangle_it 1.341 r_angle_refined_deg 1.217 r_mcbond_it 0.865 r_xyhbond_nbd_refined 0.348 r_nbtor_refined 0.308 r_nbd_refined 0.217 r_symmetry_hbond_refined 0.205 r_symmetry_vdw_refined 0.177 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 3490 Nucleic Acid Atoms Solvent Atoms 503 Heterogen Atoms 122
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing