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CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC BRANCHED-CHAIN AMINOTRANSFERASE (BCAT1) IN COMPLEX WITH PLP AND SMALL MOLECULE INHIBITOR COMPOUND 38
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 3 DAYS AT 10 MILLIMOLAR. CRYO: RESERVOIR SOLUTION COMPLEMENTED WITH 20 % (V/V) GLYCEROL AND 10 MILLIMOLAR INHIBITOR.
Crystal Properties Matthews coefficient Solvent content 2.16 43.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.425 α = 90 b = 103.001 β = 90 c = 109.432 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 2017-07-04 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 1.6 48.32 99.8 0.075 0.999 17.3 6.6 99549 28
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 1.6 1.7 1.06 0.726 1.7
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 1.6 48.32 97447 2101 99.85 0.1749 0.1742 0.1839 0.2052 0.2111 RANDOM 23.601
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] -3.38 1.57 1.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.895 r_dihedral_angle_4_deg 16.537 r_dihedral_angle_3_deg 12.204 r_dihedral_angle_1_deg 6.657 r_angle_refined_deg 1.257 r_angle_other_deg 1.251 r_chiral_restr 0.058 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.895 r_dihedral_angle_4_deg 16.537 r_dihedral_angle_3_deg 12.204 r_dihedral_angle_1_deg 6.657 r_angle_refined_deg 1.257 r_angle_other_deg 1.251 r_chiral_restr 0.058 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5772 Nucleic Acid Atoms Solvent Atoms 865 Heterogen Atoms 94
Software Software Software Name Purpose XDS data reduction PHASER phasing REFMAC refinement PDB_EXTRACT data extraction pointless data scaling