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Crystal Structure of the E9 DNase Domain with a Mutant Immunity Protein IM9 (Y55F)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EMV PDB Entry 1EMV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.3 277 24% (W/V) PEG 4K, 100mM SODIUM ACETATE BUFFER pH 5.3, temperature 277K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.06 40.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.698 α = 90 b = 52.444 β = 90 c = 86.898 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 ADSC QUANTUM 4 2000-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 0.87 SRS PX9.6
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 1.7 20 92.3 0.024 52.2 21360 21360
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) 1.7 1.76 95.9 0.046 2172
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 1EMV 1.7 9.94 21260 21260 1101 92.62 0.166 0.166 0.164 0.1746 0.204 0.2094 RANDOM 12.382
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.89 r_dihedral_angle_4_deg 16.923 r_dihedral_angle_3_deg 12.831 r_dihedral_angle_1_deg 5.52 r_scangle_it 3.361 r_scbond_it 2.123 r_angle_refined_deg 1.209 r_mcangle_it 1.136 r_mcbond_it 0.72 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.89 r_dihedral_angle_4_deg 16.923 r_dihedral_angle_3_deg 12.831 r_dihedral_angle_1_deg 5.52 r_scangle_it 3.361 r_scbond_it 2.123 r_angle_refined_deg 1.209 r_mcangle_it 1.136 r_mcbond_it 0.72 r_nbtor_refined 0.298 r_nbd_refined 0.195 r_symmetry_vdw_refined 0.168 r_symmetry_hbond_refined 0.164 r_metal_ion_refined 0.158 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.089 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1696 Nucleic Acid Atoms Solvent Atoms 404 Heterogen Atoms 6
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOLREP phasing