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Crystal structure of Bacillus subtilis TenA Y112F mutant complexed with formyl aminomethyl pyrimidine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YAF PDB entry 1yaf
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.1 100 mM acetate pH 4.1, 0.6 - 1.0 M 1,6-hexanediol, 0.01 M CoCl2
Crystal Properties Matthews coefficient Solvent content 2.08 40.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.625 α = 90 b = 58.625 β = 90 c = 296.469 γ = 90
Symmetry Space Group P 41 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 ADSC QUANTUM 315 2006-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9792 APS 24-ID-C
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 2.2 50 96.3 0.061 0.061 10.6 8.3 26664 26664
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 2.28 73.7 0.315 0.315 2.6 4.8 1972
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 PDB entry 1yaf 2.2 41.7 26547 2224 96.28 0.2 0.197 0.1944 0.233 0.2294 RANDOM 44.894
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] 1.34 1.34 -2.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.505 r_dihedral_angle_4_deg 21.58 r_dihedral_angle_3_deg 15.464 r_dihedral_angle_1_deg 4.522 r_scangle_it 1.628 r_scbond_it 1.053 r_angle_refined_deg 0.954 r_mcangle_it 0.837 r_mcbond_it 0.49 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.505 r_dihedral_angle_4_deg 21.58 r_dihedral_angle_3_deg 15.464 r_dihedral_angle_1_deg 4.522 r_scangle_it 1.628 r_scbond_it 1.053 r_angle_refined_deg 0.954 r_mcangle_it 0.837 r_mcbond_it 0.49 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.183 r_nbd_refined 0.18 r_xyhbond_nbd_refined 0.139 r_symmetry_hbond_refined 0.113 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3703 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 30
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction CNS phasing