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Effector Binding Domain of BenM (crystals generated 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 9 PEG 8000, TAPS, LiCl, imidazole, tris, NaCl, cis,cis-muconate, glycerol, pH 9, Microbatch under oil
Crystal Properties Matthews coefficient Solvent content 4.36 71.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.048 α = 90 b = 70.048 β = 90 c = 187.683 γ = 90
Symmetry Space Group P 43 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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM .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 2.2 70.014 99.9 0.063 65.96 20.9 24724 24724 43.75363
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 2.2 2.28 99.9 99.9 0.769 5.92 2381
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 2.2 70.014 23294 23294 1218 99.582 0.1779 0.1779 0.1763 0.1766 0.2094 0.2095 RANDOM 42.296
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] 0.223 0.223 -0.447
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.267 r_dihedral_angle_4_deg 14.525 r_dihedral_angle_3_deg 12.528 r_dihedral_angle_1_deg 4.812 r_scangle_it 3.242 r_scbond_it 2.099 r_mcangle_it 1.072 r_angle_refined_deg 0.915 r_mcbond_it 0.515 r_scangle_other 0.416
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.267 r_dihedral_angle_4_deg 14.525 r_dihedral_angle_3_deg 12.528 r_dihedral_angle_1_deg 4.812 r_scangle_it 3.242 r_scbond_it 2.099 r_mcangle_it 1.072 r_angle_refined_deg 0.915 r_mcbond_it 0.515 r_scangle_other 0.416 r_angle_other_deg 0.309 r_nbtor_refined 0.295 r_symmetry_vdw_other 0.217 r_nbd_refined 0.162 r_symmetry_vdw_refined 0.152 r_symmetry_hbond_refined 0.1 r_xyhbond_nbd_refined 0.099 r_scbond_other 0.099 r_nbd_other 0.097 r_nbtor_other 0.075 r_chiral_restr 0.057 r_mcangle_other 0.023 r_bond_refined_d 0.007 r_gen_planes_refined 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1722 Nucleic Acid Atoms Solvent Atoms 252 Heterogen Atoms 44
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing