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CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC BRANCHED-CHAIN AMINOTRANSFERASE (BCAT1) IN COMPLEX WITH PLP AND INHIBITOR COMPOUND 2
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 5 DAYS AT 10 MILLIMOLAR. CRYO: RESERVOIR SOLUTION COMPLEMENTED WITH 20 % (V/V) GLYCEROL AND 10 MILLIMOLAR INHIBITOR
Crystal Properties Matthews coefficient Solvent content 2.69 54.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.069 α = 90 b = 110.431 β = 103.2 c = 107.043 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS3 6M 2016-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 2.38 47.12 98.5 0.219 0.983 6.45 3.44 72443 33.37
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 2.38 2.52 96.2 0.911 0.639 1.65 3.49
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 2.38 45.24 70342 2101 98.5 0.2218 0.2206 0.2252 0.2626 0.2615 RANDOM 35.883
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] 1.77 3.36 -2.75 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.214 r_dihedral_angle_4_deg 17.993 r_dihedral_angle_3_deg 14.822 r_dihedral_angle_1_deg 6.818 r_angle_refined_deg 1.243 r_angle_other_deg 1.09 r_chiral_restr 0.044 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.214 r_dihedral_angle_4_deg 17.993 r_dihedral_angle_3_deg 14.822 r_dihedral_angle_1_deg 6.818 r_angle_refined_deg 1.243 r_angle_other_deg 1.09 r_chiral_restr 0.044 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11532 Nucleic Acid Atoms Solvent Atoms 510 Heterogen Atoms 152
Software Software Software Name Purpose REFMAC refinement XDS data reduction PDB_EXTRACT data extraction pointless data scaling PHASER phasing