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BenM effector binding domain
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 2.6 52.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.412 α = 90 b = 66.615 β = 90 c = 116.549 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 0.97937 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.908 58.321 29271 27.81656
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 1.9 1.97 22.5 0.434
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 1.908 58.321 27770 27770 1461 73.559 0.192 0.19004 0.19 0.1964 0.234 0.2488 Random 28.476
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] -0.395 2.568 -2.173
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.409 r_dihedral_angle_4_deg 14.923 r_dihedral_angle_3_deg 13.968 r_dihedral_angle_1_deg 5.937 r_scangle_it 2.79 r_scbond_it 2.1 r_angle_refined_deg 1.226 r_mcangle_it 1.203 r_scangle_other 1.191 r_mcbond_it 0.893
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.409 r_dihedral_angle_4_deg 14.923 r_dihedral_angle_3_deg 13.968 r_dihedral_angle_1_deg 5.937 r_scangle_it 2.79 r_scbond_it 2.1 r_angle_refined_deg 1.226 r_mcangle_it 1.203 r_scangle_other 1.191 r_mcbond_it 0.893 r_scbond_other 0.795 r_angle_other_deg 0.713 r_mcangle_other 0.542 r_nbd_refined 0.176 r_nbtor_refined 0.169 r_nbd_other 0.159 r_symmetry_vdw_other 0.144 r_xyhbond_nbd_refined 0.12 r_symmetry_hbond_refined 0.111 r_symmetry_vdw_refined 0.087 r_nbtor_other 0.079 r_mcbond_other 0.067 r_chiral_restr 0.057 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 3503 Nucleic Acid Atoms Solvent Atoms 579 Heterogen Atoms 6
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing