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His257Ala mutant of dihydroorotase from E. coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XGE PDB entry 1XGE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 15-20 % PEG 3350, 0.1 M MES pH 6.0, 150 mM KCl, 75 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.36 47.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.115 α = 90 b = 79.063 β = 90 c = 180.436 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 100 IMAGE PLATE MAR scanner 345 mm plate OSMIC MIRRORS 2009-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.54178
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 1.86 50 94.4 0.079 17.2 3.3 61938 59132
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) 1.86 1.93 83.6 0.276 2.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1XGE 1.87 45.13 61919 56039 3010 95.36 0.17089 0.16929 0.1831 0.2001 0.2192 RANDOM 23.311
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] -1.69 3.78 -2.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.017 r_dihedral_angle_4_deg 15.684 r_dihedral_angle_3_deg 12.027 r_dihedral_angle_1_deg 6.265 r_scangle_it 2.121 r_mcangle_it 1.878 r_angle_refined_deg 1.543 r_scbond_it 1.482 r_mcbond_it 1.335 r_angle_other_deg 1.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.017 r_dihedral_angle_4_deg 15.684 r_dihedral_angle_3_deg 12.027 r_dihedral_angle_1_deg 6.265 r_scangle_it 2.121 r_mcangle_it 1.878 r_angle_refined_deg 1.543 r_scbond_it 1.482 r_mcbond_it 1.335 r_angle_other_deg 1.003 r_mcbond_other 0.415 r_chiral_restr 0.085 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5274 Nucleic Acid Atoms Solvent Atoms 503 Heterogen Atoms 35
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection HKL-2000 data reduction HKL-2000 data scaling