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Crystal structure of human orotidine 5'-monophosphate decarboxylase complexed with CMP-N4-OH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QCM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 1.6M-1.7M Ammonium sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.09 41.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.78 α = 90 b = 61.64 β = 112.08 c = 71.37 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 MARMOSAIC 300 mm CCD DCM with cryo-cooled 1st crystal sagittally bent 2nd crystal followed by vertically focusing 2011-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.979490 CLSI 08ID-1
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 1.54 50 85 0.046 13.96 70712 -3 31.727
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 1.54 1.58 32.7 0.015 0.44
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 MOLECULAR REPLACEMENT THROUGHOUT 2qcm 1.8 66.08 50390 2633 99.02 0.1952 0.19 0.191 0.223 0.2243 RANDOM 29.1315
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] 1.44 1.81 -1.68 1.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.426 r_dihedral_angle_4_deg 19.76 r_dihedral_angle_3_deg 14.676 r_dihedral_angle_1_deg 6.443 r_scangle_it 5.262 r_scbond_it 3.667 r_angle_refined_deg 2.215 r_mcangle_it 2.177 r_mcbond_it 1.364 r_chiral_restr 0.268
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.426 r_dihedral_angle_4_deg 19.76 r_dihedral_angle_3_deg 14.676 r_dihedral_angle_1_deg 6.443 r_scangle_it 5.262 r_scbond_it 3.667 r_angle_refined_deg 2.215 r_mcangle_it 2.177 r_mcbond_it 1.364 r_chiral_restr 0.268 r_bond_refined_d 0.028 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3916 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 52
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction Macromolecular data collection