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SHMT from Streptococcus thermophilus Tyr55Ser variant as internal aldimine and as non-covalent complex with D-Ser
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 5mM
D-serine 100mM
Cacodylate 0.1M ph 6.5
Sodium citrate 0.85M
Crystal Properties Matthews coefficient Solvent content 4.24 70.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 199.956 α = 90 b = 113.657 β = 94.13 c = 132.479 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 PIXEL DECTRIS PILATUS 2M 2015-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.9697 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.33 47.85 76.01 0.95 41.89 1.59 80329
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.565 0.95
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 4WXG 2.5 47.85 73924 3838 76.01 0.1788 0.1763 0.1805 0.2265 0.228 RANDOM 40.372
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] -2.82 -3.26 -0.13 3.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.002 r_dihedral_angle_4_deg 16.246 r_dihedral_angle_3_deg 16.187 r_dihedral_angle_1_deg 7.208 r_angle_refined_deg 1.587 r_angle_other_deg 1.286 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.002 r_dihedral_angle_4_deg 16.246 r_dihedral_angle_3_deg 16.187 r_dihedral_angle_1_deg 7.208 r_angle_refined_deg 1.587 r_angle_other_deg 1.286 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12472 Nucleic Acid Atoms Solvent Atoms 376 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction XPREP data reduction PHASER phasing