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2.75 Angstrom Resolution Crystal Structure of Putative Orotidine-monophosphate-decarboxylase from Toxoplasma gondii.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QW4 PDB entry 3QW4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.3 295 Protein: 7.7 mG/mL, 0.5 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3, 0.02M Magnesium chloride, 0.02M UMP
Screen: JCSG+(C3), 0.2M Ammonium nitrate pH 6.3, 20% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.09 41.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.477 α = 90 b = 115.477 β = 90 c = 152.055 γ = 120
Symmetry Space Group P 61 2 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 Beryllium lenses 2013-08-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2.75 30 100 0.124 24.2 14.1 16220 16220 -3 53.3
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) 1 2.75 2.8 99.9 0.591 5.3 14.3 797
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3QW4 2.75 29.1 15330 15330 809 99.83 0.19092 0.19092 0.18817 0.24602 0.2266 RANDOM 46.175
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] 1.55 0.77 1.55 -5.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.304 r_dihedral_angle_4_deg 20.794 r_dihedral_angle_3_deg 13.497 r_long_range_B_refined 6.39 r_long_range_B_other 6.389 r_scangle_other 4.165 r_mcangle_it 3.373 r_mcangle_other 3.372 r_scbond_it 2.592 r_scbond_other 2.589
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.304 r_dihedral_angle_4_deg 20.794 r_dihedral_angle_3_deg 13.497 r_long_range_B_refined 6.39 r_long_range_B_other 6.389 r_scangle_other 4.165 r_mcangle_it 3.373 r_mcangle_other 3.372 r_scbond_it 2.592 r_scbond_other 2.589 r_dihedral_angle_1_deg 2.182 r_mcbond_it 2.023 r_mcbond_other 2.012 r_angle_refined_deg 1.628 r_angle_other_deg 1.394 r_chiral_restr 0.082 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 r_gen_planes_other 0.006 r_bond_other_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4381 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 42
Software Software Software Name Purpose Blu-Ice data collection BALBES phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling