☰ Navigation Tabs
Crystal structure of the effector binding domain of a BenM variant (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 microbatch under oil 288.2 Precipitant: 0.015 M magnesium acetate, 0.05 M sodium cacodlylate, 1.7 M ammonium sulfate
Protein: 20 mM tris HCl, 0.5 M NaCl, pH 7.9, 10% glycerol
Equal volumes mixed, microbatch under oil. The growing crystallization solution was in pH 6 and the protein solution was in pH 7.9 condition, temperature 288.2K
Crystal Properties Matthews coefficient Solvent content 2.4 49.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.937 α = 90 b = 66.506 β = 90 c = 117.495 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 2005-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
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 1.85 50 99.7 0.073 9.1 5.1 44035
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 1.85 1.92 99.3 99.3 0.484 4.8
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) 1.85 44 43982 41766 2216 99.62 0.167 0.167 0.165 0.1831 0.204 0.1759 RANDOM 19.128
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] 1.75 -0.49 -1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.318 r_dihedral_angle_3_deg 11.159 r_dihedral_angle_4_deg 9.713 r_dihedral_angle_1_deg 5.735 r_scangle_it 3.512 r_scbond_it 2.654 r_mcangle_it 1.306 r_angle_refined_deg 1.085 r_mcbond_it 0.917 r_angle_other_deg 0.731
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.318 r_dihedral_angle_3_deg 11.159 r_dihedral_angle_4_deg 9.713 r_dihedral_angle_1_deg 5.735 r_scangle_it 3.512 r_scbond_it 2.654 r_mcangle_it 1.306 r_angle_refined_deg 1.085 r_mcbond_it 0.917 r_angle_other_deg 0.731 r_nbd_refined 0.194 r_symmetry_vdw_other 0.173 r_nbd_other 0.169 r_nbtor_refined 0.169 r_symmetry_hbond_refined 0.146 r_symmetry_vdw_refined 0.115 r_xyhbond_nbd_refined 0.113 r_mcbond_other 0.087 r_nbtor_other 0.079 r_chiral_restr 0.059 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 3439 Nucleic Acid Atoms Solvent Atoms 578 Heterogen Atoms 52
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data scaling MOLREP phasing