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Crystal structure of Chromobacterium violaceum aminotransferase in complex with PLP-pyruvate adduct
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BA4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 290 12.5% PEG 8000 and 50 mM HEPES pH 7.5
10 mM PLP, 5 mM pyruvate
Crystal Properties Matthews coefficient Solvent content 1.99 38.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.33 α = 103.56 b = 61.38 β = 89.38 c = 116.48 γ = 105.42
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2008-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9700 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.6 39.43 76.1 0.999 14.9 4.7 156999
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.64 23 0.861 2.5 4.3
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4ba4 1.6 39.43 156996 7878 76.103 0.229 0.2273 0.2612 0.2293 17.71
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 r_dihedral_angle_2_deg 31.102 r_dihedral_angle_4_deg 15.685 r_dihedral_angle_3_deg 13.417 r_dihedral_angle_1_deg 6.894 r_lrange_it 6.767 r_scangle_it 2.043 r_mcangle_it 1.667 r_angle_refined_deg 1.422 r_scbond_it 1.254 r_mcbond_it 1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.102 r_dihedral_angle_4_deg 15.685 r_dihedral_angle_3_deg 13.417 r_dihedral_angle_1_deg 6.894 r_lrange_it 6.767 r_scangle_it 2.043 r_mcangle_it 1.667 r_angle_refined_deg 1.422 r_scbond_it 1.254 r_mcbond_it 1.01 r_symmetry_nbd_refined 0.326 r_nbtor_refined 0.299 r_metal_ion_refined 0.29 r_symmetry_metal_ion_refined 0.225 r_nbd_refined 0.211 r_symmetry_xyhbond_nbd_refined 0.196 r_xyhbond_nbd_refined 0.16 r_ncsr_local_group_4 0.078 r_ncsr_local_group_1 0.071 r_ncsr_local_group_6 0.071 r_ncsr_local_group_3 0.07 r_ncsr_local_group_5 0.066 r_chiral_restr 0.06 r_ncsr_local_group_2 0.057 r_bond_refined_d 0.013 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14296 Nucleic Acid Atoms Solvent Atoms 2031 Heterogen Atoms 213
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing DM phasing