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Crystal Structure of the Dioxygen-bound Heme Oxygenase from Corynebacterium diphtheriae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.1 303 MES, Ammonium sulfate, pH 6.1, VAPOR DIFFUSION, temperature 303K
Crystal Properties Matthews coefficient Solvent content 2.26 50.292557
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.003 α = 90 b = 62.969 β = 100.96 c = 107.49 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 IMAGE PLATE RIGAKU RAXIS 2003-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.85 50 100 0.071 22 3.8 60634 60627
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.85 1.92 100 0.343 4.1 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1.85 40 54446 6150 99.96 0.15703 0.15705 0.15302 0.1662 0.19252 0.2031 RANDOM 11.618
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] 0.11 0.38 -0.01 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.973 r_scangle_it 4.871 r_scbond_it 3.092 r_mcangle_it 1.916 r_angle_refined_deg 1.781 r_angle_other_deg 1.264 r_mcbond_it 1.069 r_symmetry_vdw_other 0.3 r_symmetry_vdw_refined 0.27 r_nbd_other 0.251
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.973 r_scangle_it 4.871 r_scbond_it 3.092 r_mcangle_it 1.916 r_angle_refined_deg 1.781 r_angle_other_deg 1.264 r_mcbond_it 1.069 r_symmetry_vdw_other 0.3 r_symmetry_vdw_refined 0.27 r_nbd_other 0.251 r_nbd_refined 0.231 r_symmetry_hbond_refined 0.2 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.111 r_metal_ion_refined 0.109 r_nbtor_other 0.09 r_bond_refined_d 0.02 r_gen_planes_other 0.018 r_gen_planes_refined 0.014 r_bond_other_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5012 Nucleic Acid Atoms Solvent Atoms 449 Heterogen Atoms 218
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling CNS phasing