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Crystal structure of the YdhT protein from Bacillus subtilis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 3.5 294 100mM Citric acid pH 3.5, 25% PEG 3350, VAPOR DIFFUSION, temperature 294K
Crystal Properties Matthews coefficient Solvent content 1.82 32.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.728 α = 90 b = 69.619 β = 91.09 c = 72.505 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 MAR CCD 165 mm 2008-02-16 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 1.269 72.548 95.5 0.095 0.095 15.1 7.6 145644 145644 9.6
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) 1.269 1.33 88.5 0.439 0.439 3.3 6.9 19656
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 SAD THROUGHOUT 1.269 20 145624 145624 7331 96.26 0.151 0.149 0.1528 0.172 0.1762 RANDOM 14.12
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 0.09 0.24 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.977 r_dihedral_angle_4_deg 17.23 r_dihedral_angle_3_deg 11.903 r_dihedral_angle_1_deg 5.849 r_sphericity_free 3.14 r_scangle_it 2.608 r_sphericity_bonded 1.829 r_scbond_it 1.821 r_mcangle_it 1.346 r_angle_refined_deg 1.197
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.977 r_dihedral_angle_4_deg 17.23 r_dihedral_angle_3_deg 11.903 r_dihedral_angle_1_deg 5.849 r_sphericity_free 3.14 r_scangle_it 2.608 r_sphericity_bonded 1.829 r_scbond_it 1.821 r_mcangle_it 1.346 r_angle_refined_deg 1.197 r_rigid_bond_restr 1.062 r_mcbond_it 0.873 r_nbtor_refined 0.309 r_nbd_refined 0.2 r_xyhbond_nbd_refined 0.142 r_symmetry_hbond_refined 0.142 r_symmetry_vdw_refined 0.132 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5381 Nucleic Acid Atoms Solvent Atoms 592 Heterogen Atoms 39
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction SHELXCD phasing SHELXE model building