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Structure of human SHMT2 protein mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PVF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7.4 291 0.2M Ammonium sulfate, 0.1M Bis-Tris (pH 7.0), 20%(w/v) Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 3.55 65.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.655 α = 90 b = 158.655 β = 90 c = 209.358 γ = 120
Symmetry Space Group P 65 2 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 CCD ADSC QUANTUM 315 2016-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NFPSS BEAMLINE BL19U1 0.979 NFPSS BL19U1
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 2.85 50 100 0.837 28.35 2 27966
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 4pvf 2.85 50 26552 1414 75.68 0.17973 0.17697 0.1806 0.23129 0.2306 RANDOM 39.622
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 -0.04 -0.07 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.608 r_dihedral_angle_4_deg 17.283 r_dihedral_angle_3_deg 16.838 r_dihedral_angle_1_deg 6.646 r_long_range_B_refined 3.739 r_long_range_B_other 3.713 r_mcangle_it 1.944 r_mcangle_other 1.944 r_scangle_other 1.669 r_angle_refined_deg 1.243
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.608 r_dihedral_angle_4_deg 17.283 r_dihedral_angle_3_deg 16.838 r_dihedral_angle_1_deg 6.646 r_long_range_B_refined 3.739 r_long_range_B_other 3.713 r_mcangle_it 1.944 r_mcangle_other 1.944 r_scangle_other 1.669 r_angle_refined_deg 1.243 r_mcbond_it 1.113 r_mcbond_other 1.113 r_angle_other_deg 0.929 r_scbond_it 0.928 r_scbond_other 0.923 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6883 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction XDS data scaling MOLREP phasing