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Crystal structure of a heme oxygenase (HmuO) from Corynebacterium diphtheriae complexed with heme in the ferric state
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.8 303 ammonium sulfate, NaI, MES, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 303K
Crystal Properties Matthews coefficient Solvent content 2.18 43.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.559 α = 90 b = 62.838 β = 100.86 c = 107.661 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 98 CCD RIGAKU JUPITER 210 mirrors 2001-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45PX 0.9 SPring-8 BL45PX
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 1.3 99 85 0.034 18.08 261943 146822
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) 1.3 1.34 58.6 0.297 0.87
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 THROUGHOUT 1.4 12 111789 111789 12385 90.11 0.168 0.168 0.16541 0.1674 0.19187 0.194 RANDOM 15.799
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] 0.01 0.3 0.47 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 13.124 r_scangle_it 3.897 r_dihedral_angle_1_deg 3.587 r_sphericity_free 2.594 r_scbond_it 2.464 r_sphericity_bonded 1.933 r_angle_refined_deg 1.736 r_mcangle_it 1.705 r_rigid_bond_restr 1.349 r_angle_other_deg 1.347
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 13.124 r_scangle_it 3.897 r_dihedral_angle_1_deg 3.587 r_sphericity_free 2.594 r_scbond_it 2.464 r_sphericity_bonded 1.933 r_angle_refined_deg 1.736 r_mcangle_it 1.705 r_rigid_bond_restr 1.349 r_angle_other_deg 1.347 r_mcbond_it 1.006 r_nbtor_other 0.551 r_symmetry_vdw_other 0.252 r_nbd_refined 0.238 r_xyhbond_nbd_refined 0.189 r_nbd_other 0.187 r_symmetry_hbond_refined 0.178 r_symmetry_vdw_refined 0.152 r_xyhbond_nbd_other 0.136 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_symmetry_hbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4996 Nucleic Acid Atoms Solvent Atoms 657 Heterogen Atoms 185
Software Software Software Name Purpose Jupiter210 data collection SCALEPACK data scaling AMoRE phasing REFMAC refinement JUPITER210 data reduction