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Crystal structure of DFA-IIIase from Arthrobacter chlorophenolicus A6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2INU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 287 10% PEG 3350, 0.1M Sodium malonate (pH 4.2)
Crystal Properties Matthews coefficient Solvent content 4.34 71.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.348 α = 90 b = 134.348 β = 90 c = 78.554 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2014-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2 50 99.8 21.8 5.4 54535
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03
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 2inu 2 38.37 51734 2799 99.8 0.11091 0.10934 0.13948 0.1541 RANDOM 29.319
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] 5.76 5.76 -11.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.293 r_dihedral_angle_4_deg 18.984 r_sphericity_free 14.251 r_dihedral_angle_3_deg 14.235 r_dihedral_angle_1_deg 7.984 r_sphericity_bonded 5.905 r_long_range_B_refined 3.147 r_long_range_B_other 3.122 r_scangle_other 2.973 r_scbond_it 2.805
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.293 r_dihedral_angle_4_deg 18.984 r_sphericity_free 14.251 r_dihedral_angle_3_deg 14.235 r_dihedral_angle_1_deg 7.984 r_sphericity_bonded 5.905 r_long_range_B_refined 3.147 r_long_range_B_other 3.122 r_scangle_other 2.973 r_scbond_it 2.805 r_scbond_other 2.805 r_mcangle_it 2.58 r_mcangle_other 2.58 r_rigid_bond_restr 2.568 r_mcbond_it 2.238 r_mcbond_other 2.219 r_angle_refined_deg 1.462 r_angle_other_deg 0.817 r_chiral_restr 0.094 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3291 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing