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Crystal structure of a heme oxygenase (HmuO) from Corynebacterium diphtheriae complexed with heme in the ferrous 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 2.49 50.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.865 α = 90 b = 62.837 β = 101.02 c = 107.208 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 2002-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45PX SPring-8 BL45PX
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 1.5 44 99 0.064 0.064 4.8 2.3 110939
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) 1.5 1.58 98.7 0.306 0.306 2.2 2.3
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MR THROUGHOUT 1.5 12 66791 105106 5579 98.89 0.178 0.177 0.2094 0.202 0.2273 RANDOM 16.11
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] -0.05 0.027 -0.01 0.026
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 11.668 r_scangle_it 4.211 r_sphericity_free 3.453 r_dihedral_angle_1_deg 3.064 r_scbond_it 2.724 r_sphericity_bonded 2.538 r_mcangle_it 1.902 r_angle_refined_deg 1.709 r_rigid_bond_restr 1.468 r_mcbond_it 1.179
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 11.668 r_scangle_it 4.211 r_sphericity_free 3.453 r_dihedral_angle_1_deg 3.064 r_scbond_it 2.724 r_sphericity_bonded 2.538 r_mcangle_it 1.902 r_angle_refined_deg 1.709 r_rigid_bond_restr 1.468 r_mcbond_it 1.179 r_angle_other_deg 0.833 r_symmetry_vdw_refined 0.242 r_nbd_refined 0.233 r_symmetry_vdw_other 0.226 r_nbd_other 0.184 r_xyhbond_nbd_refined 0.161 r_symmetry_hbond_refined 0.114 r_chiral_restr 0.085 r_bond_refined_d 0.015 r_xyhbond_nbd_other 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbtor_other r_symmetry_hbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4974 Nucleic Acid Atoms Solvent Atoms 380 Heterogen Atoms 172
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling AMoRE phasing REFMAC refinement CCP4 data scaling