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Crystal structure of ternary complex of Plasmodium vivax SHMT with D-serine and folinic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4O6Z PDB ENTRY 4O6Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 297 PEG4000, 0.06-0.12 M sodium chloride, 0.1 M Tris-HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.34 47.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.619 α = 90 b = 58.115 β = 90 c = 236.614 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC QUANTUM 315r 2010-11-03 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0 NSRRC BL13B1
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 2.4 30 94.6 0.047 30.3 2.5 51056
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 2.4 2.49 84.9 0.172 1.8 4506
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 4O6Z 2.4 30 51056 2518 93.88 0.2049 0.1996 0.1993 0.2523 0.1964 RANDOM 43.375
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] 2.25 0.18 2.54 -4.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.148 r_dihedral_angle_4_deg 20.098 r_dihedral_angle_3_deg 16.772 r_dihedral_angle_1_deg 5.799 r_angle_refined_deg 1.382 r_chiral_restr 0.09 r_bond_refined_d 0.008 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10374 Nucleic Acid Atoms Solvent Atoms 268 Heterogen Atoms 178
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling