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Structure of YTNJ from Bacillus subtilis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 1.5M NaCitrate, 0.1M Hepes pH 7.5, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.6 65.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.941 α = 90 b = 85.941 β = 90 c = 196.298 γ = 90
Symmetry Space Group P 43 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 2003-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 8-BM 0.9197 APS 8-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.104 20 99.2 0.095 16.4 9.8 43243 43146 -3 37.1
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 2.104 2.17 99.8 0.36 5.4
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.104 20 43146 43146 2179 99.12 0.20775 0.20775 0.20668 0.22801 0.2712 RANDOM 39.766
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] 2.09 2.09 -4.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.134 r_dihedral_angle_4_deg 19.955 r_dihedral_angle_3_deg 15.843 r_dihedral_angle_1_deg 5.743 r_scangle_it 2.762 r_scbond_it 1.951 r_angle_refined_deg 1.178 r_mcangle_it 1.128 r_mcbond_it 0.988 r_angle_other_deg 0.794
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.134 r_dihedral_angle_4_deg 19.955 r_dihedral_angle_3_deg 15.843 r_dihedral_angle_1_deg 5.743 r_scangle_it 2.762 r_scbond_it 1.951 r_angle_refined_deg 1.178 r_mcangle_it 1.128 r_mcbond_it 0.988 r_angle_other_deg 0.794 r_symmetry_vdw_other 0.251 r_nbd_refined 0.207 r_nbd_other 0.188 r_symmetry_hbond_refined 0.159 r_xyhbond_nbd_refined 0.154 r_mcbond_other 0.139 r_symmetry_vdw_refined 0.102 r_nbtor_other 0.087 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3068 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing REFMAC refinement