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2.06 Angstrom resolution crystal structure of a short chain dehydrogenase from Bacillus anthracis str. 'Ames Ancestor' in complex with NAD-acetone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YDE PDB entry 1YDE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 Protein was mixed at 1:1 v/v ratio with 30% PEG 2000 MME, 0.1M Na Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.34 47.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.757 α = 90 b = 168.156 β = 90 c = 107.194 γ = 90
Symmetry Space Group P 21 21 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 CCD MARMOSAIC 300 mm CCD Be Lenses/Diamond Laue Mono 2009-06-04 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) 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 2.05 30 100 0.123 15.7 7.5 148152 148152 -3 22.3
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 2.05 2.09 100 0.596 4.2 7.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB entry 1YDE 2.06 29.95 139804 139804 7388 99.97 0.16326 0.16326 0.16105 0.1817 0.20538 0.2217 RANDOM 14.228
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] 2.64 -3.51 0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.939 r_dihedral_angle_4_deg 12.213 r_dihedral_angle_3_deg 10.364 r_scangle_it 3.899 r_dihedral_angle_1_deg 3.631 r_scbond_it 2.562 r_angle_refined_deg 1.664 r_mcangle_it 1.342 r_angle_other_deg 0.951 r_mcbond_it 0.803
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.939 r_dihedral_angle_4_deg 12.213 r_dihedral_angle_3_deg 10.364 r_scangle_it 3.899 r_dihedral_angle_1_deg 3.631 r_scbond_it 2.562 r_angle_refined_deg 1.664 r_mcangle_it 1.342 r_angle_other_deg 0.951 r_mcbond_it 0.803 r_mcbond_other 0.26 r_chiral_restr 0.106 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16766 Nucleic Acid Atoms Solvent Atoms 1210 Heterogen Atoms 389
Software Software Software Name Purpose Blu-Ice data collection BALBES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling