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Crystal structure of exonuclease I in complex with inhibitor BCBP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C95 PDB entry 3C95
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 20 mg/mL Protein, 18-27% PEG 4000, 0.1-0.15 M MgCl2, Saturated inhibitor in DMSO soaked 4-5 days, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.37 48.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.823 α = 90 b = 91.966 β = 90 c = 106.28 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 MARMOSAIC 300 mm CCD 2007-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97869 APS 21-ID-D
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 1.55 50 93 0.071 34.5 5.7 72323 72323 19.9
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 1.55 1.61 85.9 0.36 2.69 2.1 6559
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 3C95 1.55 26.91 68067 68067 3594 92.76 0.1739 0.1739 0.17219 0.1729 0.20709 0.211 RANDOM 18.973
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] 1.07 -0.5 -0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.698 r_dihedral_angle_4_deg 14.775 r_dihedral_angle_3_deg 11.677 r_dihedral_angle_1_deg 5.479 r_sphericity_free 4.539 r_scangle_it 3.776 r_scbond_it 2.427 r_sphericity_bonded 2.413 r_mcangle_it 1.713 r_angle_refined_deg 1.361
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.698 r_dihedral_angle_4_deg 14.775 r_dihedral_angle_3_deg 11.677 r_dihedral_angle_1_deg 5.479 r_sphericity_free 4.539 r_scangle_it 3.776 r_scbond_it 2.427 r_sphericity_bonded 2.413 r_mcangle_it 1.713 r_angle_refined_deg 1.361 r_rigid_bond_restr 1.194 r_mcbond_it 1.005 r_angle_other_deg 0.877 r_mcbond_other 0.403 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3702 Nucleic Acid Atoms Solvent Atoms 492 Heterogen Atoms 41
Software Software Software Name Purpose PHASER phasing REFMAC refinement MAR345 data collection HKL-2000 data reduction SCALEPACK data scaling