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BenM effector binding domain with its effector, cis,cis-muconate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F6P PDB Entry 2F6P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 microbatch under oil 288 PEG 4000, ammonium sulfate, sodium acetate, NaCl, tris, glycerol, imidazole, microbatch under oil, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.38 48.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.741 α = 90 b = 65.777 β = 90 c = 117.974 γ = 90
Symmetry Space Group P 21 21 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 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 1.00727 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 1.5 59.028 59.1 0.053 25.8 4.46 54680 54680 24.51076
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.49 1.55 0.6 0.3 53
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 2F6P 1.9 59.028 35808 35808 1788 88.526 0.209 0.209 0.207 0.2159 0.2503 0.2597 RANDOM 30.727
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] 0.556 1.313 -1.869
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.341 r_dihedral_angle_4_deg 16.683 r_dihedral_angle_3_deg 13.188 r_dihedral_angle_1_deg 5.434 r_scangle_it 3.565 r_scbond_it 2.662 r_scangle_other 1.527 r_mcangle_it 1.475 r_angle_refined_deg 1.094 r_mcbond_it 1.037
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.341 r_dihedral_angle_4_deg 16.683 r_dihedral_angle_3_deg 13.188 r_dihedral_angle_1_deg 5.434 r_scangle_it 3.565 r_scbond_it 2.662 r_scangle_other 1.527 r_mcangle_it 1.475 r_angle_refined_deg 1.094 r_mcbond_it 1.037 r_scbond_other 1.023 r_angle_other_deg 0.74 r_mcangle_other 0.65 r_nbd_refined 0.181 r_symmetry_vdw_other 0.173 r_nbd_other 0.169 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.146 r_symmetry_hbond_refined 0.136 r_mcbond_other 0.097 r_symmetry_vdw_refined 0.09 r_nbtor_other 0.079 r_chiral_restr 0.061 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3517 Nucleic Acid Atoms Solvent Atoms 481 Heterogen Atoms 37
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing