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BenM effector-Binding domain crystallized from high pH conditions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F6G PDB ENTRY 2F6G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 10 PEG 4000, glycerol, imidazole, tris, CAPS, KBr, NaCl, benzoate, pH 10, Microbatch under oil
Crystal Properties Matthews coefficient Solvent content 4.6 73.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.06 α = 90 b = 106.401 β = 90 c = 184.306 γ = 90
Symmetry Space Group C 2 2 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 MARRESEARCH 2003-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97935 APS 19-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 2.7 92.06 98.4 0.093 28.1 7.16 25480 25480 53.78698
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 2.7 2.8 98.1 98.1 0.421 5.85 2494
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 (All) 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 2F6G 2.7 92.06 24162 24162 1299 98.15 0.151 0.151 0.148 0.1799 0.196 0.2179 RANDOM 32.036
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] 1.56 -0.06 -1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.052 r_dihedral_angle_3_deg 16.152 r_dihedral_angle_4_deg 14.854 r_dihedral_angle_1_deg 5.47 r_scangle_it 4.887 r_scbond_it 3.176 r_mcangle_it 1.639 r_angle_refined_deg 1.083 r_mcbond_it 0.74 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.052 r_dihedral_angle_3_deg 16.152 r_dihedral_angle_4_deg 14.854 r_dihedral_angle_1_deg 5.47 r_scangle_it 4.887 r_scbond_it 3.176 r_mcangle_it 1.639 r_angle_refined_deg 1.083 r_mcbond_it 0.74 r_nbtor_refined 0.307 r_symmetry_hbond_refined 0.204 r_nbd_refined 0.189 r_symmetry_vdw_refined 0.149 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3503 Nucleic Acid Atoms Solvent Atoms 455 Heterogen Atoms 68
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing