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1.5 Angstrom Crystal Structure of Shikimate Dehydrogenase 1 from Peptoclostridium difficile.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FBT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 Protein: 10.6 mg/ml, 0.01M Tris-HCL (pH 8.3); Screen: Classics II (F3), 0.064M Sodium citrate (pH 7.0), 0.1M HEPES (pH 7.0), 10% (w/v) PEG 5000 MME; Cryo: 1:1 (v/v), 50% Sucrose : screen solution.
Crystal Properties Matthews coefficient Solvent content 2.21 44.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.221 α = 77.98 b = 47.053 β = 76.44 c = 74.736 γ = 89.09
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 MARMOSAIC 300 mm CCD 2015-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 1.5 30 96.1 0.038 0.038 29 3.9 82004 -3 23.6
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 1.5 1.53 94.5 0.454 3.1 4
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 3FBT 1.5 29.7 77919 4078 95.92 0.16451 0.16345 0.1726 0.1846 0.1932 RANDOM 38.531
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] -0.21 0.2 -0.15 -0.91 -0.46 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.257 r_dihedral_angle_4_deg 18.564 r_dihedral_angle_3_deg 9.867 r_long_range_B_refined 7.646 r_long_range_B_other 7.463 r_scangle_other 3.81 r_dihedral_angle_1_deg 3.087 r_mcangle_it 2.715 r_mcangle_other 2.715 r_scbond_it 2.505
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.257 r_dihedral_angle_4_deg 18.564 r_dihedral_angle_3_deg 9.867 r_long_range_B_refined 7.646 r_long_range_B_other 7.463 r_scangle_other 3.81 r_dihedral_angle_1_deg 3.087 r_mcangle_it 2.715 r_mcangle_other 2.715 r_scbond_it 2.505 r_scbond_other 2.449 r_mcbond_it 1.728 r_mcbond_other 1.727 r_angle_refined_deg 1.373 r_angle_other_deg 0.754 r_chiral_restr 0.086 r_gen_planes_refined 0.02 r_gen_planes_other 0.016 r_bond_refined_d 0.009 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 4200 Nucleic Acid Atoms Solvent Atoms 423 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement BLU-MAX data collection HKL-3000 data reduction HKL-3000 data scaling MrBUMP phasing