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Structure and inhibition of orotidine 5'-phosphate decarboxylase from plasmodium falciparum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F84 PDB entry 2F84
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 Protein at 10mg/ml (in 25mM HEPES and 150mM NaCl)combined with equal volume of solution containing 100mM sodium acetate and 2M sodium formate., pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.39 48.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.929 α = 90 b = 104.087 β = 113.82 c = 62.42 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 IMAGE PLATE MAR scanner 345 mm plate osmic mirrors 2006-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.22 15.01 99 0.102 9.6 4.3 32849 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.22 2.28 95.4 0.319 3.2 3
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 PDB entry 2F84 2.223 15.01 32849 1741 98.98 0.20478 0.20129 0.1839 0.27095 0.2464 RANDOM 39.319
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] -0.08 0.57 -0.42 0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.097 r_dihedral_angle_4_deg 22.991 r_dihedral_angle_3_deg 15.11 r_scangle_it 6.481 r_dihedral_angle_1_deg 6.307 r_scbond_it 5.05 r_mcangle_it 3.041 r_mcbond_it 2.476 r_angle_refined_deg 1.267 r_angle_other_deg 0.811
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.097 r_dihedral_angle_4_deg 22.991 r_dihedral_angle_3_deg 15.11 r_scangle_it 6.481 r_dihedral_angle_1_deg 6.307 r_scbond_it 5.05 r_mcangle_it 3.041 r_mcbond_it 2.476 r_angle_refined_deg 1.267 r_angle_other_deg 0.811 r_mcbond_other 0.635 r_nbd_refined 0.203 r_symmetry_vdw_other 0.193 r_nbtor_refined 0.187 r_nbd_other 0.169 r_symmetry_vdw_refined 0.149 r_xyhbond_nbd_refined 0.146 r_symmetry_hbond_refined 0.126 r_nbtor_other 0.085 r_chiral_restr 0.078 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9877 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling