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Plasmodium vivax SHMT bound with PLP-glycine and GS557
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 2.37 48.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.858 α = 90 b = 58.79 β = 90.03 c = 234.062 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 2016-03-25 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) 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 2.24 50.01 96.2 0.026 28.2 3 64408
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.33 84.3 0.137 0.975 2.1
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 2.24 50.01 56670 6361 93.57 0.2458 0.24 0.2405 0.2971 0.2902 RANDOM 30.28
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] 0.27 0.03 -0.06 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.331 r_dihedral_angle_3_deg 18.272 r_dihedral_angle_4_deg 17.868 r_dihedral_angle_1_deg 5.839 r_mcangle_it 2.442 r_mcbond_it 1.508 r_mcbond_other 1.508 r_angle_refined_deg 1.471 r_angle_other_deg 0.976 r_chiral_restr 0.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.331 r_dihedral_angle_3_deg 18.272 r_dihedral_angle_4_deg 17.868 r_dihedral_angle_1_deg 5.839 r_mcangle_it 2.442 r_mcbond_it 1.508 r_mcbond_other 1.508 r_angle_refined_deg 1.471 r_angle_other_deg 0.976 r_chiral_restr 0.075 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 10374 Nucleic Acid Atoms Solvent Atoms 254 Heterogen Atoms 170
Software Software Software Name Purpose HKL-2000 data collection HKL-2000 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction