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SHMT from Streptococcus thermophilus Tyr55Thr variant in complex with D-Serine both as external aldimine and as non-covalent complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WXB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 PLP 0.1 mm
D-Serine 100 mm
cacodylate 0.1 M, pH 6.5
sodium citrate 0.85 M
Crystal Properties Matthews coefficient Solvent content 4.21 70.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 200.795 α = 90 b = 112.93 β = 93.1 c = 131.918 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 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 2.1 98 99.3 0.05 17.9 6.5 165927
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 2.2 0.05
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 4WXB 2.12 47.76 157619 8296 99.33 0.2391 0.2368 0.239 0.2836 0.2843 RANDOM 55.166
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] 0.07 -0.02 0.26 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.128 r_dihedral_angle_3_deg 16.677 r_dihedral_angle_4_deg 15.474 r_dihedral_angle_1_deg 7.532 r_angle_refined_deg 1.647 r_angle_other_deg 1.293 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.128 r_dihedral_angle_3_deg 16.677 r_dihedral_angle_4_deg 15.474 r_dihedral_angle_1_deg 7.532 r_angle_refined_deg 1.647 r_angle_other_deg 1.293 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12476 Nucleic Acid Atoms Solvent Atoms 381 Heterogen Atoms 91
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction XDS data scaling PHASER phasing