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Crystal Structure of Human Orotidine 5'-monophosphate Decarboxylase Complexed with XMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P1F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.4 293 Ammonium Sulfate, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.06 40.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.857 α = 90 b = 61.976 β = 112.96 c = 70.514 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 225 mm CCD DCM with cryo-cooled 1st crystal sagittally bent 2nd crystal followed by vertically focusing mirror 2007-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97934 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.8 50 97.8 0.111 0.111 6.6 4.9 50616 49502
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.86 90.9 0.456 0.456 1.64 3.4 4656
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 2P1F 1.8 24.2 49353 48026 2579 97.31 0.18723 0.18505 0.1842 0.22844 0.227 RANDOM 20.266
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] 1.11 1.77 -1.04 1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.246 r_dihedral_angle_4_deg 16.098 r_dihedral_angle_3_deg 13.454 r_dihedral_angle_1_deg 6.078 r_scangle_it 3.716 r_scbond_it 2.354 r_angle_refined_deg 1.52 r_mcangle_it 1.377 r_mcbond_it 1.001 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.246 r_dihedral_angle_4_deg 16.098 r_dihedral_angle_3_deg 13.454 r_dihedral_angle_1_deg 6.078 r_scangle_it 3.716 r_scbond_it 2.354 r_angle_refined_deg 1.52 r_mcangle_it 1.377 r_mcbond_it 1.001 r_nbtor_refined 0.3 r_symmetry_vdw_refined 0.219 r_nbd_refined 0.202 r_xyhbond_nbd_refined 0.137 r_symmetry_hbond_refined 0.133 r_chiral_restr 0.104 r_bond_refined_d 0.01 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3934 Nucleic Acid Atoms Solvent Atoms 311 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement MxDC data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing Coot model building