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Structure of the substrate-free HmuO, HO from Corynebacterium diphtheriae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 293 PEG8000, Sodium Acetate, Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.32 47.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.489 α = 90 b = 61.916 β = 90 c = 63.086 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 95 CCD ADSC QUANTUM 315 2004-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 1.8 50 98.4 21348 21006
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.86 97.4
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 MOLECULAR REPLACEMENT THROUGHOUT 1.8 30 21006 18909 2065 98.26 0.17868 0.17868 0.17471 0.1863 0.21615 0.2267 RANDOM 20.97
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] -1.12 -0.3 1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.499 r_dihedral_angle_3_deg 14.874 r_dihedral_angle_4_deg 13.696 r_dihedral_angle_1_deg 5.544 r_scangle_it 4.426 r_scbond_it 2.796 r_mcangle_it 1.97 r_angle_other_deg 1.838 r_angle_refined_deg 1.729 r_mcbond_it 1.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.499 r_dihedral_angle_3_deg 14.874 r_dihedral_angle_4_deg 13.696 r_dihedral_angle_1_deg 5.544 r_scangle_it 4.426 r_scbond_it 2.796 r_mcangle_it 1.97 r_angle_other_deg 1.838 r_angle_refined_deg 1.729 r_mcbond_it 1.091 r_symmetry_vdw_other 0.356 r_mcbond_other 0.292 r_symmetry_vdw_refined 0.287 r_nbd_refined 0.233 r_nbd_other 0.2 r_metal_ion_refined 0.2 r_nbtor_refined 0.188 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.123 r_symmetry_hbond_refined 0.123 r_nbtor_other 0.096 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1670 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 38
Software Software Software Name Purpose ADSC data collection CNS refinement REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing