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Crystal structure of Plasmodium falciparum orotidine 5'-monophosphate decarboxylase complexed with 6-amino-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 8.8 293 PEG 1000, ammonium phosphate, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.89 35.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.802 α = 90 b = 83.131 β = 90 c = 89.983 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 ADSC QUANTUM 210 2006-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.97710 CHESS A1
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 1.47 50 99.5 0.061 0.061 10.9 7.2 103172 99916
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 1.47 1.5 91.8 0.497 0.497 2.88 5.5 4685
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2Q8L 1.47 50 97966 5151 99.5 0.16414 0.16272 0.19105 0.1845 RANDOM 17.292
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] 0.09 -0.16 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.787 r_dihedral_angle_4_deg 22.868 r_dihedral_angle_3_deg 13.286 r_dihedral_angle_1_deg 6.091 r_scangle_it 3.739 r_scbond_it 2.542 r_mcangle_it 1.577 r_angle_refined_deg 1.54 r_mcbond_it 0.992 r_nbtor_refined 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.787 r_dihedral_angle_4_deg 22.868 r_dihedral_angle_3_deg 13.286 r_dihedral_angle_1_deg 6.091 r_scangle_it 3.739 r_scbond_it 2.542 r_mcangle_it 1.577 r_angle_refined_deg 1.54 r_mcbond_it 0.992 r_nbtor_refined 0.319 r_nbd_refined 0.222 r_symmetry_vdw_refined 0.222 r_symmetry_hbond_refined 0.187 r_xyhbond_nbd_refined 0.132 r_chiral_restr 0.108 r_bond_refined_d 0.01 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5345 Nucleic Acid Atoms Solvent Atoms 597 Heterogen Atoms 91
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement Coot model building HKL-2000 data reduction HKL-2000 data scaling