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Plasmodium vivax SHMT bound with PLP-glycine and GS256
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 2.33 47.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.943 α = 90 b = 58.297 β = 90.02 c = 233.613 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 RAYONIX MX300HE 2015-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1 NSRRC BL15A1
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 30 95.8 0.057 13.6 4.1 62386
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 80.3 0.353 0.906 3.6
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 30 56081 6303 95.37 0.2229 0.2152 0.2108 0.2926 0.2882 RANDOM 48.311
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] 2.2 0.1 2.02 -4.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.074 r_dihedral_angle_3_deg 18.597 r_dihedral_angle_4_deg 18.457 r_dihedral_angle_1_deg 5.703 r_mcangle_it 4.342 r_scbond_it 3.127 r_mcbond_it 2.83 r_angle_refined_deg 1.595 r_chiral_restr 0.096 r_bond_refined_d 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.074 r_dihedral_angle_3_deg 18.597 r_dihedral_angle_4_deg 18.457 r_dihedral_angle_1_deg 5.703 r_mcangle_it 4.342 r_scbond_it 3.127 r_mcbond_it 2.83 r_angle_refined_deg 1.595 r_chiral_restr 0.096 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10374 Nucleic Acid Atoms Solvent Atoms 391 Heterogen Atoms 167
Software Software Software Name Purpose Blu-Ice data collection HKL-2000 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction