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Crystal structure of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3G18
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 25% PEG 3350, 0.1M Tris-HCl, 0.2M magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.14 42.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.772 α = 90 b = 64.07 β = 115.46 c = 61.639 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 ADSC QUANTUM 4 2009-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.97915 NSLS X4A
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 1.4 25 91.6 0.069 75761 75761 14
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 MOLECULAR REPLACEMENT THROUGHOUT 3G18 1.4 24.87 75761 75761 3807 91.6 0.186 0.184 0.184 0.1832 0.195 0.1922 RANDOM 14.1
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] -2.74 -1.28 2.43 0.31
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.9 c_scangle_it 2.69 c_scbond_it 1.81 c_mcangle_it 1.36 c_angle_deg 1.2 c_improper_angle_d 0.91 c_mcbond_it 0.91 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3299 Nucleic Acid Atoms Solvent Atoms 271 Heterogen Atoms 44
Software Software Software Name Purpose ADSC data collection BALBES phasing CNS refinement DENZO data reduction SCALEPACK data scaling