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Crystal structure of W27-Fab in complex with an epitope peptide from serine hydroxymethyltransferase (SHMT)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9WN2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 0.2 M Magnecium Acetate, 0.1 M Sodium Cacodylate pH6.3, 22% PEG10,000,20%(v/v) Glycerol
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.37 α = 90 b = 140.655 β = 90 c = 180.979 γ = 90
Symmetry Space Group P 21 21 21
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 X 16M 2019-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.999994 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.35 47.295 99.7 0.066 0.999 16.69 6.5 64977
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.49 98.7 0.831 0.9 2.7 6.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 9WN2 2.35 45.79 1.36 64932 3249 99.65 0.2246 0.2227 0.223 0.2617 0.2601 68.5
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.5674 f_angle_d 0.5033 f_chiral_restr 0.0417 f_plane_restr 0.0039 f_bond_d 0.0021
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9482 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 21
Software Software Software Name Purpose PHENIX refinement XDS data reduction