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Crystal Structure of the E9 DNase Domain with a Mutant Immunity Protein IM9 (D51A)
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 2.1 41.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.903 α = 90 b = 88.248 β = 91.92 c = 52.235 γ = 90
Symmetry Space Group P 1 21 1
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 1.6 20 96.3 0.027 34.4 51260 51260
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) 1.6 1.66 84.5 0.045 4468
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB Entry 1EMV 1.6 19.86 51228 51228 2598 96.21 0.187 0.187 0.185 0.232 0.2681 RANDOM 15.426
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.306 r_dihedral_angle_4_deg 17.686 r_dihedral_angle_3_deg 13.353 r_dihedral_angle_1_deg 5.806 r_scangle_it 3.309 r_scbond_it 2.149 r_mcangle_it 1.248 r_angle_refined_deg 1.229 r_mcbond_it 0.805 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.306 r_dihedral_angle_4_deg 17.686 r_dihedral_angle_3_deg 13.353 r_dihedral_angle_1_deg 5.806 r_scangle_it 3.309 r_scbond_it 2.149 r_mcangle_it 1.248 r_angle_refined_deg 1.229 r_mcbond_it 0.805 r_nbtor_refined 0.297 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.19 r_xyhbond_nbd_refined 0.147 r_symmetry_hbond_refined 0.146 r_metal_ion_refined 0.113 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3373 Nucleic Acid Atoms Solvent Atoms 686 Heterogen Atoms 12
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOLREP phasing