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CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC BRANCHED-CHAIN AMINOTRANSFERASE (BCAT1) IN COMPLEX WITH PLP AND SMALL MOLECULE INHIBITOR COMPOUND 21(5-F)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ABJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 PROTEIN AT 17 MG/ML IN 10 MILLIMOLAR TRIS-HCL PH 8.0, 100 MILLIMOLAR NACL, 3 MILLIMOLAR DTT. PROTEIN PREINCUBATED OVER NIGHT AT 293 K WITH 10 MILLIMOLAR 3-PHENYL-PROPIONATE, 3 MILLIMOLAR DTT AND 1.5 MILLIMOLAR PLP.
DROPS MADE FROM 1 MICROLITER PROTEIN AND 1 MICROLITER RESERVOIR (225 MILLIMOLAR MGCL2, 16-20 % (W/V) PEG 3350). INHIBITOR SOAKED INTO PREFORMED CRYSTALS FOR 1 DAY AT 10 MILLIMOLAR. CRYO: RESERVOIR SOLUTION COMPLEMENTED WITH 20 % (V/V) GLYCEROL AND 10 MILLIMOLAR INHIBITOR.
Crystal Properties Matthews coefficient Solvent content 2.24 45.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.723 α = 90 b = 106.188 β = 90 c = 109.326 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 PILATUS 6M 2017-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.7 47.76 99.7 0.063 1 20.6 6.6 85902 34
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.8 99.2 1.296 0.709 1.6 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 2ABJ 1.7 41.55 83801 2101 99.66 0.1904 0.1896 0.1965 0.2237 0.2274 RANDOM 33.509
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] -5.92 3.5 2.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.936 r_dihedral_angle_4_deg 16.619 r_dihedral_angle_3_deg 14.474 r_dihedral_angle_1_deg 6.776 r_angle_refined_deg 1.381 r_angle_other_deg 1.251 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.936 r_dihedral_angle_4_deg 16.619 r_dihedral_angle_3_deg 14.474 r_dihedral_angle_1_deg 6.776 r_angle_refined_deg 1.381 r_angle_other_deg 1.251 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5739 Nucleic Acid Atoms Solvent Atoms 593 Heterogen Atoms 99
Software Software Software Name Purpose XDS data reduction pointless data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing