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Plasmodium vivax SHMT(C346A) bound with PLP-glycine and MF057
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4TMR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 8.5 298 PEG4000, 0.06-0.12M NaCl, 0.1M Tris-HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.32 46.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.486 α = 90 b = 58.089 β = 90.05 c = 234.749 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 315 2016-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 94.2 0.019 0.024 0.014 31.9 2.3 51013
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 84 0.073 0.097 0.063 0.992 1.9
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 4TMR 2.4 30 45356 5104 94.36 0.2711 0.2669 0.2636 0.3091 0.302 RANDOM 32.68
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] 0.11 -0.08 0.02 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.116 r_dihedral_angle_4_deg 19.857 r_dihedral_angle_3_deg 18.589 r_dihedral_angle_1_deg 5.914 r_angle_refined_deg 1.495 r_angle_other_deg 0.979 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.116 r_dihedral_angle_4_deg 19.857 r_dihedral_angle_3_deg 18.589 r_dihedral_angle_1_deg 5.914 r_angle_refined_deg 1.495 r_angle_other_deg 0.979 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10371 Nucleic Acid Atoms Solvent Atoms 335 Heterogen Atoms 188
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing