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Crystal structure of adenosylmethionine-8-amino-7-oxononanoate aminotransferase from Methanocaldococcus jannaschii DSM 2661
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DOD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.2M MgCl2; 0.1M Tris pH 8.5; 19% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.13 42.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.232 α = 106.11 b = 61.38 β = 93.48 c = 63.069 γ = 96.47
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 2017-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.969 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.8 60.56 88.5 0.102 0.126 0.072 0.989 6.4 2.7 71599
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 86.1 0.431 0.533 0.309 0.755 2.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3DOD 1.8 60.56 68050 3545 88.54 0.1796 0.1774 0.2217 0.2285 RANDOM 21.987
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] -2.36 0.47 1.15 -0.56 1.03 1.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.09 r_dihedral_angle_4_deg 22.389 r_dihedral_angle_3_deg 16.055 r_dihedral_angle_1_deg 6.67 r_angle_refined_deg 1.842 r_chiral_restr 0.123 r_bond_refined_d 0.013 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6916 Nucleic Acid Atoms Solvent Atoms 446 Heterogen Atoms 3
Software Software Software Name Purpose MOSFLM data reduction Aimless data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction