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X-Ray Crystal Structure of Human Heme Oxygenase-1 in Complex with 1-(1H-imidazol-1-yl)-4,4-diphenyl-2 butanone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N3U 1N3U Chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 100 mM HEPES (pH 7.5), 2.2 M ammonium sulfate, 0.95% 1,6-hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.12 41.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.61 α = 90 b = 74.98 β = 90 c = 115.28 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 3.3 Undulator (Undulator A) 2011-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.979300 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 2.75 20 96.1 0.099 9.26 2.63 11070 -3
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 2.75 2.8 97.2 0.972 1.4 2.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1N3U Chain A 2.85 19.82 12468 10516 554 100 0.22516 0.22312 0.26377 0.2326 RANDOM 55.859
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] -0.76 -2.13 2.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.114 r_dihedral_angle_3_deg 16.523 r_dihedral_angle_4_deg 13.759 r_dihedral_angle_1_deg 4.231 r_scangle_it 0.912 r_angle_refined_deg 0.91 r_mcangle_it 0.602 r_scbond_it 0.503 r_mcbond_it 0.328 r_chiral_restr 0.061
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.114 r_dihedral_angle_3_deg 16.523 r_dihedral_angle_4_deg 13.759 r_dihedral_angle_1_deg 4.231 r_scangle_it 0.912 r_angle_refined_deg 0.91 r_mcangle_it 0.602 r_scbond_it 0.503 r_mcbond_it 0.328 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 3498 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 138
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data scaling