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Crystal structure of transcription regulator from Bacteroides thetaiotaomicron VPI-5482 at 2.15 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 273 4.0M NaFormate, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 3.86 67.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.98 α = 90 b = 115.98 β = 90 c = 119.639 γ = 120
Symmetry Space Group P 65 2 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 4 Double-crystal monochromator (Si 111), toroid 2005-05-05 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL1-5 0.979094, 0.918381 SSRL BL1-5
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 2.1 29.91 99.9 0.088 0.088 6.4 6.8 28282
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 2.1 2.15 98.8 0.766 0.766 1 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.15 29.2 25047 1332 99.87 0.18 0.177 0.1841 0.228 0.233 RANDOM 38.566
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] -1.33 -0.66 -1.33 1.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.444 r_dihedral_angle_4_deg 15.613 r_dihedral_angle_3_deg 12.987 r_scangle_it 7.474 r_scbond_it 5.604 r_dihedral_angle_1_deg 5.56 r_mcangle_it 3.226 r_mcbond_it 2.395 r_angle_refined_deg 1.406 r_angle_other_deg 0.781
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.444 r_dihedral_angle_4_deg 15.613 r_dihedral_angle_3_deg 12.987 r_scangle_it 7.474 r_scbond_it 5.604 r_dihedral_angle_1_deg 5.56 r_mcangle_it 3.226 r_mcbond_it 2.395 r_angle_refined_deg 1.406 r_angle_other_deg 0.781 r_mcbond_other 0.529 r_symmetry_vdw_other 0.24 r_symmetry_hbond_refined 0.232 r_nbd_refined 0.21 r_nbtor_refined 0.181 r_symmetry_vdw_refined 0.179 r_nbd_other 0.173 r_xyhbond_nbd_refined 0.143 r_nbtor_other 0.085 r_chiral_restr 0.084 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1863 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling SOLVE phasing