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Plasmodium vivax SHMT bound with PLP-glycine and GS654
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 PEG 4000, 0.06-0.12 M NaCl, 0.1 M Tris-HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.39 48.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.075 α = 90 b = 58.928 β = 90.06 c = 234.83 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 2.26 50.01 96.3 0.02 32.4 3.7 63448
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 2.26 2.34 81.8 0.126 0.982 2.9
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 2.26 50.01 57000 6374 95.82 0.2563 0.2501 0.2486 0.3115 0.3013 RANDOM 29.185
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] 0.05 0.03 -0.07 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.708 r_dihedral_angle_3_deg 18.848 r_dihedral_angle_4_deg 18.686 r_dihedral_angle_1_deg 5.643 r_mcangle_it 2.532 r_mcbond_it 1.562 r_mcbond_other 1.561 r_angle_refined_deg 1.544 r_angle_other_deg 0.998 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.708 r_dihedral_angle_3_deg 18.848 r_dihedral_angle_4_deg 18.686 r_dihedral_angle_1_deg 5.643 r_mcangle_it 2.532 r_mcbond_it 1.562 r_mcbond_other 1.561 r_angle_refined_deg 1.544 r_angle_other_deg 0.998 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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 272 Heterogen Atoms 173
Software Software Software Name Purpose HKL-2000 data collection HKL-2000 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction