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Crystal structure of Plasmodium falciparum orotidine 5'-phosphate decarboxylase covalently modified by 6-azido-UMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q8L PDB entry 2Q8L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9.2 293 100mM Ammonium phosphate, 27% PEG 1000, pH 9.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.9 35.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.928 α = 90 b = 83.354 β = 90 c = 89.872 γ = 90
Symmetry Space Group P 21 21 2
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 sagitally 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 1.9 50 95.37 0.085 0.085 11.4 5.2 44155 44155
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 1.9 1.97 97.9 0.459 0.459 3.45 5.1 4703
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 PDB entry 2Q8L 1.9 24.68 44155 44155 2357 95.37 0.17445 0.17445 0.17202 0.1722 0.2193 0.2191 RANDOM 22.075
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] 0.49 -0.19 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.745 r_dihedral_angle_4_deg 24.013 r_dihedral_angle_3_deg 14.035 r_dihedral_angle_1_deg 5.871 r_scangle_it 3.725 r_scbond_it 2.53 r_mcangle_it 1.613 r_angle_refined_deg 1.518 r_mcbond_it 1.017 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.745 r_dihedral_angle_4_deg 24.013 r_dihedral_angle_3_deg 14.035 r_dihedral_angle_1_deg 5.871 r_scangle_it 3.725 r_scbond_it 2.53 r_mcangle_it 1.613 r_angle_refined_deg 1.518 r_mcbond_it 1.017 r_nbtor_refined 0.316 r_nbd_refined 0.228 r_symmetry_vdw_refined 0.222 r_xyhbond_nbd_refined 0.149 r_symmetry_hbond_refined 0.146 r_chiral_restr 0.107 r_bond_refined_d 0.01 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5308 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement Macromolecular data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing