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crystal structure of Plasmodium vivax orotidine 5-monophosphate decarboxylase with 6-aza-UMP bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FFC PDB ENTRY 2FFC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 297 30% PEG 4K, 0.2 M Sodium Acetate, 0.1M Tris HCl, pH 8.0, VAPOR DIFFUSION, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.13 42.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.731 α = 90 b = 82.151 β = 90 c = 59.739 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 IMAGE PLATE RIGAKU RAXIS IV++ VariMax HR 2006-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E 1.54
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 1.86 32.09 91.8 0.1 0.1 9.8 7 27267 27267 25.8
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 1.86 1.89 54 0.823 0.823 1.57 5.1 793
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 PDB ENTRY 2FFC 1.86 32.09 26323 26323 896 91.66 0.1899 0.1899 0.18838 0.1866 0.23614 0.2331 RANDOM 26.776
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] 0.45 -1.17 0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.258 r_dihedral_angle_4_deg 17.892 r_dihedral_angle_3_deg 14.348 r_dihedral_angle_1_deg 5.883 r_scangle_it 3.598 r_scbond_it 2.283 r_angle_refined_deg 1.456 r_mcangle_it 1.41 r_mcbond_it 0.884 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.258 r_dihedral_angle_4_deg 17.892 r_dihedral_angle_3_deg 14.348 r_dihedral_angle_1_deg 5.883 r_scangle_it 3.598 r_scbond_it 2.283 r_angle_refined_deg 1.456 r_mcangle_it 1.41 r_mcbond_it 0.884 r_nbtor_refined 0.304 r_nbd_refined 0.202 r_symmetry_hbond_refined 0.181 r_symmetry_vdw_refined 0.171 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.105 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 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 2560 Nucleic Acid Atoms Solvent Atoms 262 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-2000 data scaling PHASER phasing Coot model building