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Crystal structure of Plasmodium falciparum orotidine 5'-monophosphate decarboxylase covalently modified by 2-prime-fluoro-6-iodo-UMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q8L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 293 PEG 1000, ammonium phosphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.89 34.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.473 α = 90 b = 83.519 β = 90 c = 89.614 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 sagittally bent 2nd crystal followed by vertically focusing mirror. 2007-08-16 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 1.75 50 97.7 0.067 0.067 11 4.6 60004 57246
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 1.75 1.81 98.6 0.464 0.464 2.55 3.6 5957
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 2Q8L 1.75 50 56929 3035 97.57 0.16413 0.16229 0.1618 0.19829 0.198 RANDOM 17.807
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] 0.29 -0.02 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.423 r_dihedral_angle_4_deg 21.104 r_dihedral_angle_3_deg 14.048 r_dihedral_angle_1_deg 6.013 r_scangle_it 3.872 r_scbond_it 2.678 r_mcangle_it 1.543 r_angle_refined_deg 1.508 r_mcbond_it 1.006 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.423 r_dihedral_angle_4_deg 21.104 r_dihedral_angle_3_deg 14.048 r_dihedral_angle_1_deg 6.013 r_scangle_it 3.872 r_scbond_it 2.678 r_mcangle_it 1.543 r_angle_refined_deg 1.508 r_mcbond_it 1.006 r_nbtor_refined 0.316 r_symmetry_hbond_refined 0.216 r_nbd_refined 0.21 r_symmetry_vdw_refined 0.202 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.109 r_bond_refined_d 0.01 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5360 Nucleic Acid Atoms Solvent Atoms 454 Heterogen Atoms 54
Software Software Software Name Purpose MxDC data collection MOLREP phasing REFMAC refinement Coot model building HKL-2000 data reduction HKL-2000 data scaling