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Crystal Structure of BdbD from Bacillus subtilis (reduced)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 27% PEG2000, 0.1M ammonium acetate, 0.1M MES, pH6.5, 1mM DTT,cryo-protected with 20% Ethylene glycol
Crystal Properties Matthews coefficient Solvent content 1.9 35.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.774 α = 90 b = 43.399 β = 107.4 c = 54.658 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 28.21 97.8 0.052 15 3.5 27450 27450 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.5 1.58 89.5 0.267 3.4 2.9 27450
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 THROUGHOUT 1.5 26.08 26211 26211 1385 98.83 0.18776 0.18608 0.1834 0.21919 0.216 RANDOM 18.639
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] 0.26 -0.05 0.9 -1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.327 r_dihedral_angle_3_deg 14.006 r_dihedral_angle_1_deg 5.251 r_sphericity_free 4.729 r_sphericity_bonded 3.612 r_scangle_it 3.286 r_scbond_it 2.211 r_dihedral_angle_4_deg 1.856 r_mcangle_it 1.605 r_rigid_bond_restr 1.361
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.327 r_dihedral_angle_3_deg 14.006 r_dihedral_angle_1_deg 5.251 r_sphericity_free 4.729 r_sphericity_bonded 3.612 r_scangle_it 3.286 r_scbond_it 2.211 r_dihedral_angle_4_deg 1.856 r_mcangle_it 1.605 r_rigid_bond_restr 1.361 r_angle_refined_deg 1.225 r_mcbond_it 1.029 r_symmetry_vdw_refined 0.312 r_nbtor_refined 0.31 r_nbd_refined 0.204 r_symmetry_hbond_refined 0.135 r_xyhbond_nbd_refined 0.091 r_metal_ion_refined 0.09 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1538 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 5
Software Software Software Name Purpose ADSC data collection BP3 model building REFMAC refinement MOSFLM data reduction SCALA data scaling BP3 phasing