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Dihydroorotase from Escherichia coli: Loop Movement and Cooperativity between subunits
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J79 PDB ENTRY 1J79
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 PEG 3350, MES, potassium chloride, magnesium chloride, L-dihydroorotate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.3 45.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.582 α = 90 b = 78.826 β = 90 c = 180.222 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 MARRESEARCH mirrors 2003-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 1.9 20 92 0.056 17.4 2.5 54214 54214 31.03
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 1.9 1.97 83.8 0.256 2.8 1.6 4883
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 (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 Refinement THROUGHOUT PDB ENTRY 1J79 1.9 20 54182 51420 2762 92.29 0.17099 0.17018 0.16798 0.175 0.21067 0.2144 RANDOM 35.546
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] 0.68 1.33 -2.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.131 r_dihedral_angle_4_deg 15.567 r_dihedral_angle_3_deg 13.831 r_dihedral_angle_1_deg 6.029 r_scangle_it 1.889 r_scbond_it 1.272 r_angle_refined_deg 1.185 r_angle_other_deg 0.778 r_mcangle_it 0.759 r_mcbond_it 0.529
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.131 r_dihedral_angle_4_deg 15.567 r_dihedral_angle_3_deg 13.831 r_dihedral_angle_1_deg 6.029 r_scangle_it 1.889 r_scbond_it 1.272 r_angle_refined_deg 1.185 r_angle_other_deg 0.778 r_mcangle_it 0.759 r_mcbond_it 0.529 r_nbd_refined 0.203 r_symmetry_vdw_other 0.18 r_nbd_other 0.175 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.144 r_symmetry_hbond_refined 0.144 r_mcbond_other 0.114 r_symmetry_vdw_refined 0.112 r_nbtor_other 0.081 r_chiral_restr 0.068 r_metal_ion_refined 0.066 r_xyhbond_nbd_other 0.025 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 5384 Nucleic Acid Atoms Solvent Atoms 775 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling