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Structure of aminotransferase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EO5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 PEG 3000, MgCl2, cacodylate
Crystal Properties Matthews coefficient Solvent content 2.68 54.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.378 α = 90 b = 113.378 β = 90 c = 290.041 γ = 120
Symmetry Space Group P 65 2 2
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 2M 2018-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.8 50 100 0.133 0.138 0.035 5.3 13.9 102595
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 1.83 100 0.713 0.74 0.189 0.905 12.8
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 2eo5 1.8 49.99 97334 5134 99.98 0.1745 0.173 0.1876 0.2022 0.2081 RANDOM 26.62
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] 0.65 0.33 0.65 -2.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.066 r_dihedral_angle_3_deg 14.056 r_dihedral_angle_4_deg 13.225 r_dihedral_angle_1_deg 6.527 r_angle_refined_deg 1.685 r_angle_other_deg 1.428 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.066 r_dihedral_angle_3_deg 14.056 r_dihedral_angle_4_deg 13.225 r_dihedral_angle_1_deg 6.527 r_angle_refined_deg 1.685 r_angle_other_deg 1.428 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7108 Nucleic Acid Atoms Solvent Atoms 641 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PDB_EXTRACT data extraction PHASER phasing