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Plasmodium vivax SHMT bound with PLP-glycine and GS704
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 2.36 47.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.471 α = 90 b = 58.632 β = 90 c = 234.636 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 2016-12-14 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 2.45 30 96 0.016 0.02 0.011 30.7 2.8 49369
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 2.45 2.54 88.7 0.092 0.117 0.072 0.985 2.3
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 2.45 30 44275 4840 95.82 0.2315 0.2246 0.2227 0.2942 0.2853 RANDOM 35.504
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] 0.02 0.02 0.01 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.339 r_dihedral_angle_3_deg 20.835 r_dihedral_angle_4_deg 19.818 r_dihedral_angle_1_deg 5.282 r_angle_refined_deg 1.567 r_angle_other_deg 1.027 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.339 r_dihedral_angle_3_deg 20.835 r_dihedral_angle_4_deg 19.818 r_dihedral_angle_1_deg 5.282 r_angle_refined_deg 1.567 r_angle_other_deg 1.027 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 175 Heterogen Atoms 173
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing