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Crystal Structure of P. falciparum Orotidine 5'-monophosphate Decarboxylase Complexed with XMP
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 7.2 293 30% PEG 1000, 100mM Ammonium Phosphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.20
Crystal Properties Matthews coefficient Solvent content 1.9 35.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.902 α = 90 b = 83.582 β = 90 c = 89.793 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 2007-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 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 1.7 50 99.5 0.068 0.068 11.2 4.6 66788
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 1.7 1.76 95.6 0.394 0.394 2.6 3.5
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 2Q8L 1.7 50 64102 63705 3394 99.4 0.172 0.17 0.1684 0.205 0.204 RANDOM 18.72
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] -0.01 0.22 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.05 r_dihedral_angle_4_deg 20.515 r_dihedral_angle_3_deg 13.739 r_dihedral_angle_1_deg 6.124 r_scangle_it 3.94 r_scbond_it 2.731 r_mcangle_it 1.668 r_angle_refined_deg 1.553 r_mcbond_it 1.079 r_nbtor_refined 0.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.05 r_dihedral_angle_4_deg 20.515 r_dihedral_angle_3_deg 13.739 r_dihedral_angle_1_deg 6.124 r_scangle_it 3.94 r_scbond_it 2.731 r_mcangle_it 1.668 r_angle_refined_deg 1.553 r_mcbond_it 1.079 r_nbtor_refined 0.318 r_symmetry_vdw_refined 0.241 r_nbd_refined 0.214 r_symmetry_hbond_refined 0.158 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.112 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5352 Nucleic Acid Atoms Solvent Atoms 366 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing