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Crystal structure of branched-chain aminotransferase from thermophilic archaea Geoglobus acetivorans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EIY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 0.2M CaCl2, 0.1M Na acetate, 20% isopropanol
Crystal Properties Matthews coefficient Solvent content 2.78 55.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.65 α = 90 b = 117.65 β = 90 c = 135.98 γ = 120
Symmetry Space Group P 32 2 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 PILATUS 6M 2014-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.9 58.83 99.6 0.066 0.068 31.75 19.8 85638 -3 36.772
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 98.6 0.771 0.792 4.02
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 2EIY 1.9 101.89 81410 4226 99.64 0.1533 0.15143 0.1659 0.1879 0.1659 RANDOM 37.672
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] 0.48 0.24 0.48 -1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.672 r_dihedral_angle_4_deg 19.202 r_dihedral_angle_3_deg 14.69 r_long_range_B_refined 7.276 r_long_range_B_other 7.276 r_dihedral_angle_1_deg 6.595 r_scangle_other 5.802 r_scbond_it 4.235 r_scbond_other 4.235 r_mcangle_it 4.163
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.672 r_dihedral_angle_4_deg 19.202 r_dihedral_angle_3_deg 14.69 r_long_range_B_refined 7.276 r_long_range_B_other 7.276 r_dihedral_angle_1_deg 6.595 r_scangle_other 5.802 r_scbond_it 4.235 r_scbond_other 4.235 r_mcangle_it 4.163 r_mcangle_other 4.163 r_mcbond_it 3.384 r_mcbond_other 3.384 r_angle_refined_deg 1.988 r_angle_other_deg 1.144 r_chiral_restr 0.136 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6624 Nucleic Acid Atoms Solvent Atoms 626 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction XSCALE data scaling MOLREP phasing PDB_EXTRACT data extraction