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Plasmodium vivax SHMT bound with PLP-glycine and GS362
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 2.38 48.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.674 α = 90 b = 58.843 β = 90.14 c = 234.899 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 2016-08-14 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 2.15 30 98.8 0.028 0.033 0.017 19.1 3.6 74369
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 2.15 2.23 93.7 0.39 0.478 0.271 0.833 2.7
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 2.16 30 63482 6878 93.26 0.2482 0.2419 0.2442 0.3058 0.3017 RANDOM 30.149
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] 0.14 0.05 0.08 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.247 r_dihedral_angle_3_deg 18.757 r_dihedral_angle_4_deg 18.331 r_dihedral_angle_1_deg 5.565 r_angle_refined_deg 1.529 r_angle_other_deg 1 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.247 r_dihedral_angle_3_deg 18.757 r_dihedral_angle_4_deg 18.331 r_dihedral_angle_1_deg 5.565 r_angle_refined_deg 1.529 r_angle_other_deg 1 r_chiral_restr 0.08 r_bond_refined_d 0.011 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 10374 Nucleic Acid Atoms Solvent Atoms 380 Heterogen Atoms 161
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing