☰ Navigation Tabs
Crystal Structure of BenM_DBD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH UNDER OIL 7.5 288 Equal volumes of precipitant and protein solution. Precipitant:Crystal Screen 2 # 30 - 0.1 M HEPES pH 7.5, 10% PEG 6000, 5% MPD. Protein: 20 mM Tris base (pH 8.0), 0.5 M NaCl, 10% glycerol, 150 mM imidazole, 10 mM BME, MICROBATCH UNDER OIL, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.21 44.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.36 α = 90 b = 84.146 β = 90 c = 68.734 γ = 90
Symmetry Space Group C 2 2 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 MAR 2007-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1.0080 APS 19-ID
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 1.8 42.07 9300
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 1.8 42.07 8754 437 98.85 0.18778 0.18547 0.1982 0.23367 0.237 RANDOM 32.037
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] 0.45 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.84 r_dihedral_angle_4_deg 16.431 r_dihedral_angle_3_deg 13.434 r_scangle_it 3.739 r_dihedral_angle_1_deg 3.438 r_scbond_it 3.096 r_mcangle_it 1.503 r_angle_refined_deg 0.917 r_mcbond_it 0.72 r_chiral_restr 0.057
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.84 r_dihedral_angle_4_deg 16.431 r_dihedral_angle_3_deg 13.434 r_scangle_it 3.739 r_dihedral_angle_1_deg 3.438 r_scbond_it 3.096 r_mcangle_it 1.503 r_angle_refined_deg 0.917 r_mcbond_it 0.72 r_chiral_restr 0.057 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 704 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling