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Crystal Structure of the E9 DNase Domain with a Mutant Immunity Protein IM9 (V34A)
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 2.09 41.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.19 α = 90 b = 52.45 β = 90 c = 89.11 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 97.2 0.044 23 23064 23064
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 90.9 0.171 2125
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 19.8 23022 23022 1184 97.93 0.216 0.216 0.214 0.2198 0.256 0.2583 RANDOM 24.983
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 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.646 r_dihedral_angle_4_deg 23.587 r_dihedral_angle_3_deg 15.333 r_dihedral_angle_1_deg 5.467 r_scangle_it 4.108 r_scbond_it 2.646 r_mcangle_it 1.674 r_angle_refined_deg 1.457 r_mcbond_it 1.126 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.646 r_dihedral_angle_4_deg 23.587 r_dihedral_angle_3_deg 15.333 r_dihedral_angle_1_deg 5.467 r_scangle_it 4.108 r_scbond_it 2.646 r_mcangle_it 1.674 r_angle_refined_deg 1.457 r_mcbond_it 1.126 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.207 r_nbd_refined 0.205 r_symmetry_hbond_refined 0.192 r_xyhbond_nbd_refined 0.151 r_metal_ion_refined 0.132 r_chiral_restr 0.102 r_bond_refined_d 0.015 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1695 Nucleic Acid Atoms Solvent Atoms 201 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