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BenM effector binding domain with its effector benzoate
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 2.47 50.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.386 α = 90 b = 69.508 β = 90 c = 116.859 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 2.05 59.761 96.7 0.068 25.2 4.2 32511 32511 27.01904
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 2.05 2.12 97.5 97.5 0.599 3.8 3218
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 2.05 59.761 32187 32187 1635 95.706 0.183 0.183 0.1802 0.1911 0.2416 0.2478 RANDOM 35.916
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] 0.383 1.737 -2.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.217 r_dihedral_angle_4_deg 14.376 r_dihedral_angle_3_deg 14.247 r_dihedral_angle_1_deg 5.681 r_scangle_it 3.226 r_scbond_it 2.426 r_scangle_other 1.347 r_mcangle_it 1.317 r_angle_refined_deg 1.116 r_angle_other_deg 0.928
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.217 r_dihedral_angle_4_deg 14.376 r_dihedral_angle_3_deg 14.247 r_dihedral_angle_1_deg 5.681 r_scangle_it 3.226 r_scbond_it 2.426 r_scangle_other 1.347 r_mcangle_it 1.317 r_angle_refined_deg 1.116 r_angle_other_deg 0.928 r_mcbond_it 0.883 r_scbond_other 0.87 r_mcangle_other 0.559 r_symmetry_vdw_other 0.206 r_nbd_refined 0.185 r_nbtor_refined 0.169 r_nbd_other 0.167 r_symmetry_vdw_refined 0.151 r_chiral_restr 0.137 r_xyhbond_nbd_refined 0.131 r_symmetry_hbond_refined 0.128 r_mcbond_other 0.086 r_nbtor_other 0.081 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3471 Nucleic Acid Atoms Solvent Atoms 588 Heterogen Atoms 45
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing