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Crystal structure of Bacillus subtilis BacC Dihydroanticapsin 7-dehydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AWD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.5 291.15 0.2M Ammonium sulfate, 0.1M BIS-TRIS pH6.5, 25% w/v Polyethylene glycol 3350, 10% glycerol cryoprotectant, 0.05M Tris, 0.25M NaCl
Crystal Properties Matthews coefficient Solvent content 2.25 45.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.52 α = 90 b = 87.2 β = 101.08 c = 78.29 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 MARMOSAIC 225 mm CCD 2014-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.95372 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.187 32.95 99.6 0.071 0.998 9.2 4.1 305981 10.1
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 1.187 1.25 97.4 1.067 1.5 3.8
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 3AWD 1.19 32.95 290778 15057 99.53 0.139 0.138 0.1492 0.163 0.1689 RANDOM 18.258
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] -0.58 0.59 0.55 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.828 r_sphericity_free 36.519 r_sphericity_bonded 15.65 r_dihedral_angle_4_deg 12.687 r_dihedral_angle_3_deg 11.61 r_dihedral_angle_1_deg 5.762 r_long_range_B_refined 5.125 r_long_range_B_other 4.437 r_scangle_other 4.346 r_scbond_it 3.825
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.828 r_sphericity_free 36.519 r_sphericity_bonded 15.65 r_dihedral_angle_4_deg 12.687 r_dihedral_angle_3_deg 11.61 r_dihedral_angle_1_deg 5.762 r_long_range_B_refined 5.125 r_long_range_B_other 4.437 r_scangle_other 4.346 r_scbond_it 3.825 r_scbond_other 3.773 r_rigid_bond_restr 3.52 r_mcangle_other 2.623 r_mcangle_it 2.619 r_mcbond_it 2.13 r_mcbond_other 2.109 r_angle_refined_deg 1.583 r_angle_other_deg 1.388 r_chiral_restr 0.101 r_bond_refined_d 0.012 r_bond_other_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.006 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 7576 Nucleic Acid Atoms Solvent Atoms 987 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing