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Crystal structure of the effector binding domain of a BenM variant (BenM R156H/T157S)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F97 PDB accession code 2F97, BenM-EBD (high pH)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 296.4 Precipitant:2.0 M ammonium sulfate
Protein: 20 mM tris HCl, 0.5 M NaCl, pH 7.9, 10% glycerol
Equal volumes mixed, Microbatch under oil, temperature 296.4K
Crystal Properties Matthews coefficient Solvent content 2.5 49.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.51 α = 90 b = 66.587 β = 90 c = 117.971 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 2005-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.00000 APS 22-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 1.8 50 100 0.078 6.9 48633
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 1.8 1.86 99.77 99.9 0.464 6.3
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 accession code 2F97, BenM-EBD (high pH) 1.8 46.7 48557 46104 2453 99.95 0.171 0.171 0.168 0.1812 0.21 0.2193 RANDOM 16.201
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] 0.77 0.13 -0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.253 r_dihedral_angle_4_deg 12.756 r_dihedral_angle_3_deg 11.509 r_dihedral_angle_1_deg 5.572 r_scangle_it 3.219 r_scbond_it 2.441 r_mcangle_it 1.187 r_angle_refined_deg 0.989 r_mcbond_it 0.823 r_angle_other_deg 0.729
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.253 r_dihedral_angle_4_deg 12.756 r_dihedral_angle_3_deg 11.509 r_dihedral_angle_1_deg 5.572 r_scangle_it 3.219 r_scbond_it 2.441 r_mcangle_it 1.187 r_angle_refined_deg 0.989 r_mcbond_it 0.823 r_angle_other_deg 0.729 r_nbd_refined 0.186 r_nbtor_refined 0.167 r_nbd_other 0.16 r_symmetry_vdw_other 0.159 r_symmetry_vdw_refined 0.127 r_xyhbond_nbd_refined 0.098 r_symmetry_hbond_refined 0.093 r_nbtor_other 0.078 r_mcbond_other 0.071 r_chiral_restr 0.059 r_bond_refined_d 0.006 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 3448 Nucleic Acid Atoms Solvent Atoms 741 Heterogen Atoms 38
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data scaling MOLREP phasing