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Crystal Structure of Plasmodium Vivax Orotidine-Monophosphate-Decarboxyl UMP Bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AQW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 296 30.0% PEG 4K, 0.2M NaOAc, 0.1M Tris HCl,
VAPOR DIFFUSION, pH 8.5, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.1 41.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.817 α = 90 b = 69.588 β = 90 c = 59.338 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 SBC-3 Si 111 2005-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 1.0 APS 19-BM
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 97.7 0.052 0.052 10.2 6.8 37109 37109 29.1
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 1.72 80.3 0.612 0.612 1.6 4.7 1473
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2AQW 1.7 50 36127 36127 944 97.68 0.18825 0.18825 0.18703 0.1875 0.23444 0.1747 RANDOM 25.437
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] -0.93 0.22 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.829 r_dihedral_angle_4_deg 18.714 r_dihedral_angle_3_deg 14.237 r_dihedral_angle_1_deg 5.747 r_scangle_it 4.199 r_scbond_it 2.746 r_mcangle_it 1.719 r_angle_refined_deg 1.585 r_mcbond_it 1.179 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.829 r_dihedral_angle_4_deg 18.714 r_dihedral_angle_3_deg 14.237 r_dihedral_angle_1_deg 5.747 r_scangle_it 4.199 r_scbond_it 2.746 r_mcangle_it 1.719 r_angle_refined_deg 1.585 r_mcbond_it 1.179 r_nbtor_refined 0.31 r_nbd_refined 0.21 r_symmetry_vdw_refined 0.191 r_xyhbond_nbd_refined 0.147 r_symmetry_hbond_refined 0.146 r_chiral_restr 0.12 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 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 2570 Nucleic Acid Atoms Solvent Atoms 318 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PHASER phasing Coot model building