☰ Navigation Tabs
Crystal structure of the rat heme oxygenase (HO-1) in complex with heme binding dithiothreitol (DTT)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IVJ PDB ENTRY 1IVJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 4M Sodium Formate, 5mM Sodium azide, 100mM DTT, pH7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.48 50.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.739 α = 90 b = 65.739 β = 90 c = 120.663 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD RIGAKU JUPITER 210 2005-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.15 50 17047
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 1IVJ 2.15 30 16139 861 99.99 0.16467 0.16245 0.1747 0.20855 0.2095 RANDOM 33.27
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] 2.03 1.02 2.03 -3.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.17 r_dihedral_angle_4_deg 15.908 r_dihedral_angle_3_deg 15.434 r_dihedral_angle_1_deg 5.815 r_scangle_it 5.326 r_scbond_it 3.506 r_mcangle_it 2 r_angle_refined_deg 1.916 r_mcbond_it 1.156 r_chiral_restr 0.144
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.17 r_dihedral_angle_4_deg 15.908 r_dihedral_angle_3_deg 15.434 r_dihedral_angle_1_deg 5.815 r_scangle_it 5.326 r_scbond_it 3.506 r_mcangle_it 2 r_angle_refined_deg 1.916 r_mcbond_it 1.156 r_chiral_restr 0.144 r_bond_refined_d 0.025 r_gen_planes_refined 0.011 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 1723 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 51
Software Software Software Name Purpose CNS refinement REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing