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Structure of human SHMT1-H135N-R137A-E168N mutant at 3.6 Ang. resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BJ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 294 2 microL of 80microM protein solution in: 20 mM Hepes pH7.2, 250 mM NaCl 5% glycerol + 2 microL of reservoir:0.1 M Na Cacodilate pH6.5 - 1M Na citrate
Crystal Properties Matthews coefficient Solvent content 3.17 61.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.719 α = 90 b = 139.719 β = 90 c = 267.377 γ = 90
Symmetry Space Group P 43 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 EIGER R 4M CRL 2017-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.96770 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3.6 56.61 98.2 0.312 0.34 0.131 0.973 5.6 6.3 30938
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 3.6 3.79 99.2 1.019 1.107 0.425 0.57 6.5
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 1BJ4 3.6 50.01 29318 1545 98.02 0.263 0.2622 0.2621 0.2771 0.2807 RANDOM 74.364
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] 2.93 2.93 -5.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.068 r_dihedral_angle_4_deg 12.658 r_dihedral_angle_3_deg 12.18 r_dihedral_angle_1_deg 3.553 r_angle_refined_deg 0.638 r_angle_other_deg 0.508 r_chiral_restr 0.035 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.068 r_dihedral_angle_4_deg 12.658 r_dihedral_angle_3_deg 12.18 r_dihedral_angle_1_deg 3.553 r_angle_refined_deg 0.638 r_angle_other_deg 0.508 r_chiral_restr 0.035 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14328 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing PDB_EXTRACT data extraction