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SHMT from Streptococcus thermophilus Tyr55Ser variant in complex with PLP/L-Threonine/Lys230 gem diamine complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WXG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 PLP 0.1M
D-Threonine 100mM
Cacodylate 0.1 ph 6.5
Sodium citrate 1M
Crystal Properties Matthews coefficient Solvent content 3.51 64.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.708 α = 90 b = 114.708 β = 90 c = 192.063 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2016-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9798 ALBA XALOC
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 98.48 99.98 0.06 10.3 3.6 87017
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.058 0.06
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-Free (Depositor) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4WXG 2 98.48 87017 99.98 0.1778 0.1778 45.696
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 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.081 r_dihedral_angle_4_deg 16.968 r_dihedral_angle_3_deg 15.146 r_dihedral_angle_1_deg 6.75 r_angle_refined_deg 1.863 r_angle_other_deg 1.495 r_chiral_restr 0.096 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.081 r_dihedral_angle_4_deg 16.968 r_dihedral_angle_3_deg 15.146 r_dihedral_angle_1_deg 6.75 r_angle_refined_deg 1.863 r_angle_other_deg 1.495 r_chiral_restr 0.096 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6236 Nucleic Acid Atoms Solvent Atoms 374 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction XPREP data reduction PHASER phasing