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Crystal Structure of Ureidoglycolate Dehydrogenase from Escherichia Coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RFM Density modified experimental electron density map based on Se sites. Se sites were obtained from poor phases from a weak MR solution using a model derived from pdb entry 1RFM.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 291 15% PEG 4000, 0.1M Sodium Citrate pH 5.6, 0.06M Amonium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.38 47.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.715 α = 90 b = 129.916 β = 95.77 c = 106.468 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 100 CCD MARRESEARCH Diamond monochromator and downstream mirror 2003-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9800 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.25 19.86 80.5 0.078 6.5 1.2 213051 213051 25.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.25 2.33 72 0.284 19123
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 SAD THROUGHOUT Density modified experimental electron density map based on Se
sites. Se sites were obtained from poor phases from a weak MR solution
using a model derived from pdb entry 1RFM. 2.25 19.86 200433 9082 75.6 0.1921 0.192 0.2065 0.25 0.262 RANDOM 38.6
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] -0.44 1.74 3.28 -2.85
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.9 c_scangle_it 3.87 c_scbond_it 3.09 c_mcangle_it 2.22 c_angle_deg 1.8 c_mcbond_it 1.44 c_improper_angle_d 1.22 c_bond_d 0.018
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20836 Nucleic Acid Atoms Solvent Atoms 644 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing BEAST model building SHARP phasing RESOLVE model building CNS refinement BEAST phasing RESOLVE phasing