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Deletion 107-116 mutant of dihydroorotase from E. coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XGE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 14% PEG 3350, 0.1M MES, 75mM MgCl2, 0.15M KCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.25 45.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.296 α = 90 b = 52.296 β = 90 c = 215.995 γ = 120
Symmetry Space Group P 32 1 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2006-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.9793 APS 23-ID-B
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 1.85 40 95.9 0.077 17.4 8.2 28254 28254 40.6
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 1.85 1.9 92.5 0.63 2.6 6 1950
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 1XGE 1.85 40 28254 28254 1430 95.9 0.19379 0.19118 0.1978 0.24546 0.2485 RANDOM 51.878
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 -0.05 -0.11 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.978 r_dihedral_angle_4_deg 18.002 r_dihedral_angle_3_deg 12.628 r_dihedral_angle_1_deg 6.835 r_scangle_it 6.227 r_mcangle_it 5.193 r_scbond_it 4.786 r_mcbond_it 4.738 r_mcbond_other 1.694 r_angle_refined_deg 1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.978 r_dihedral_angle_4_deg 18.002 r_dihedral_angle_3_deg 12.628 r_dihedral_angle_1_deg 6.835 r_scangle_it 6.227 r_mcangle_it 5.193 r_scbond_it 4.786 r_mcbond_it 4.738 r_mcbond_other 1.694 r_angle_refined_deg 1.51 r_angle_other_deg 0.873 r_symmetry_vdw_other 0.235 r_nbd_refined 0.214 r_nbtor_refined 0.179 r_symmetry_vdw_refined 0.178 r_nbd_other 0.175 r_xyhbond_nbd_refined 0.143 r_symmetry_hbond_refined 0.121 r_metal_ion_refined 0.11 r_chiral_restr 0.097 r_nbtor_other 0.084 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_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 2611 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing