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Crystal structure of the E9 DNase domain with a mutant immunity protein IM9 (Y54F)
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 VAPOUR DIFFUSSION,SITTING DROP 5.3 277 24% (W/V) PEG 4K, 100mM SODIUM ACETATE BUFFER pH 5.3, VAPOUR DIFFUSSION,SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.04 39.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.232 α = 90 b = 51.929 β = 90 c = 87.674 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 MARRESEARCH 1999-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
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 1.75 20 99.1 0.042 19.1 20738 20738
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) 1.75 1.81 100 0.23 2037
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 1.75 19.41 20738 20691 1062 98.74 0.188 0.188 0.186 0.2104 0.222 0.239 RANDOM 19.194
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 35.065 r_dihedral_angle_4_deg 18.337 r_dihedral_angle_3_deg 15.096 r_dihedral_angle_1_deg 5.308 r_scangle_it 3.465 r_scbond_it 2.211 r_mcangle_it 1.299 r_angle_refined_deg 1.297 r_mcbond_it 0.813 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.065 r_dihedral_angle_4_deg 18.337 r_dihedral_angle_3_deg 15.096 r_dihedral_angle_1_deg 5.308 r_scangle_it 3.465 r_scbond_it 2.211 r_mcangle_it 1.299 r_angle_refined_deg 1.297 r_mcbond_it 0.813 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.22 r_nbd_refined 0.208 r_symmetry_hbond_refined 0.204 r_xyhbond_nbd_refined 0.159 r_metal_ion_refined 0.105 r_chiral_restr 0.094 r_bond_refined_d 0.012 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1669 Nucleic Acid Atoms Solvent Atoms 330 Heterogen Atoms 6
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing