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Crystal structure of aminotransferase CrmG from Actinoalloteichus sp. WH1-2216-6 in complex with amino donor L-Arg
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DDS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.2 M Sodium acetate, 0.1 M TRIS pH 8.5, 32%PEG 3350, 2% glycerol
Crystal Properties Matthews coefficient Solvent content 2.42 49.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.849 α = 90 b = 113.28 β = 91.74 c = 157.681 γ = 90
Symmetry Space Group C 1 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 PILATUS3 6M 2017-01-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9785 SSRF BL19U1
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 2.35 40.19 93.7 0.129 0.15 0.075 0.989 7.6 3.8 84776
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 2.35 2.39 92.6 0.593 0.685 0.335 0.777 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.35 40.19 80589 4173 93.54 0.19891 0.19688 0.2026 0.23741 0.241 RANDOM 28.151
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] 0.01 -0.18 0.56 -0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.936 r_dihedral_angle_4_deg 20.548 r_dihedral_angle_3_deg 15.165 r_dihedral_angle_1_deg 6.994 r_long_range_B_refined 6.601 r_long_range_B_other 6.601 r_scangle_other 4.9 r_mcangle_other 4.102 r_mcangle_it 4.101 r_scbond_it 3.144
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.936 r_dihedral_angle_4_deg 20.548 r_dihedral_angle_3_deg 15.165 r_dihedral_angle_1_deg 6.994 r_long_range_B_refined 6.601 r_long_range_B_other 6.601 r_scangle_other 4.9 r_mcangle_other 4.102 r_mcangle_it 4.101 r_scbond_it 3.144 r_scbond_other 3.144 r_mcbond_it 2.703 r_mcbond_other 2.701 r_angle_refined_deg 1.667 r_angle_other_deg 1.308 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 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 15815 Nucleic Acid Atoms Solvent Atoms 484 Heterogen Atoms 148
Software Software Software Name Purpose REFMAC refinement Aimless data scaling MOSFLM data reduction MOLREP phasing