☰ Navigation Tabs
X-ray structure of the WlarG aminotransferase, apo form, from Campylobacter jejune
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FRK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 100 mM MOPS (pH 7)
18-18% PEG-3350
Crystal Properties Matthews coefficient Solvent content 2.17 43.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.726 α = 90 b = 56.837 β = 90.04 c = 124.797 γ = 90
Symmetry Space Group P 1 21 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 CCD Bruker Platinum 135 montel 2016-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 50 98.8 0.093 0.093 8.4 4 197128
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.7 96.3 0.411 2 2.3 31639
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 3frk 1.6 29.97 187240 9871 98.62 0.15032 0.14833 0.18768 0.1732 RANDOM 13.501
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] 4.65 -1.27 1.72 -6.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.006 r_dihedral_angle_4_deg 16.11 r_dihedral_angle_3_deg 15.259 r_dihedral_angle_1_deg 7.38 r_long_range_B_refined 4.648 r_long_range_B_other 4.642 r_scangle_other 3.619 r_scbond_it 2.57 r_scbond_other 2.57 r_mcangle_it 2.381
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.006 r_dihedral_angle_4_deg 16.11 r_dihedral_angle_3_deg 15.259 r_dihedral_angle_1_deg 7.38 r_long_range_B_refined 4.648 r_long_range_B_other 4.642 r_scangle_other 3.619 r_scbond_it 2.57 r_scbond_other 2.57 r_mcangle_it 2.381 r_mcangle_other 2.381 r_mcbond_it 1.797 r_mcbond_other 1.797 r_angle_refined_deg 1.74 r_angle_other_deg 0.83 r_chiral_restr 0.111 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 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 11705 Nucleic Acid Atoms Solvent Atoms 712 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing