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Crystallization and structure determination of cytoplasm serine hydroxymethyltransferase (SHMT) from Pichia pastoris
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LS3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291 18% PEG8000, 0.1M MES pH 6.0, 0.2M Ca(OAc)2
Crystal Properties Matthews coefficient Solvent content 2.44 49.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.315 α = 90 b = 114.743 β = 90 c = 84.157 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 CCD ADSC QUANTUM 315 2017-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.9791 SSRF BL18U1
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 2.5 50 99.4 0.095 2.46 9.5 17959
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 2.5 2.54 0.924
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 1LS3 2.5 50 16985 883 99.4 0.22827 0.22662 0.2356 0.25995 0.2365 RANDOM 68.933
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] 9.99 -3.46 -6.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.875 r_dihedral_angle_4_deg 14.368 r_dihedral_angle_3_deg 14.327 r_long_range_B_refined 6.262 r_long_range_B_other 6.261 r_dihedral_angle_1_deg 5.468 r_mcangle_it 3.952 r_mcangle_other 3.951 r_scangle_other 3.864 r_mcbond_it 2.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.875 r_dihedral_angle_4_deg 14.368 r_dihedral_angle_3_deg 14.327 r_long_range_B_refined 6.262 r_long_range_B_other 6.261 r_dihedral_angle_1_deg 5.468 r_mcangle_it 3.952 r_mcangle_other 3.951 r_scangle_other 3.864 r_mcbond_it 2.33 r_mcbond_other 2.329 r_scbond_it 2.232 r_scbond_other 2.232 r_angle_refined_deg 1.109 r_angle_other_deg 0.878 r_chiral_restr 0.059 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 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 2794 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling BALBES phasing