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The crystal structure of the orthorhombic form of the putative HAD-hydrolase YfnB from Bacillus subtilis bound to magnesium reveals interdomain movement
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ED5 PDB entry 3ED5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 294 100mM Tris HCl pH 8.5, 30% PEG 4K, 200mM magnesium chloride, vapor diffusion, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.35 47.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.685 α = 90 b = 67.964 β = 90 c = 271.404 γ = 90
Symmetry Space Group P 21 21 21
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 2009-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97958 APS 31-ID
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 2 50 91.6 0.097 0.097 33.1 6.7 55918 51221 20.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 87.7 0.397 0.397 8.9 6.8 2392
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3ED5 2 20 55855 51018 2573 91.34 0.177 0.175 0.219 0.2128 RANDOM 23.739
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] -0.05 -1.39 1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.352 r_dihedral_angle_4_deg 22.491 r_dihedral_angle_3_deg 15.072 r_dihedral_angle_1_deg 5.811 r_scangle_it 4.282 r_scbond_it 2.73 r_mcangle_it 1.707 r_angle_refined_deg 1.484 r_mcbond_it 0.94 r_angle_other_deg 0.929
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.352 r_dihedral_angle_4_deg 22.491 r_dihedral_angle_3_deg 15.072 r_dihedral_angle_1_deg 5.811 r_scangle_it 4.282 r_scbond_it 2.73 r_mcangle_it 1.707 r_angle_refined_deg 1.484 r_mcbond_it 0.94 r_angle_other_deg 0.929 r_mcbond_other 0.254 r_chiral_restr 0.093 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5569 Nucleic Acid Atoms Solvent Atoms 405 Heterogen Atoms 14
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing