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ENDONUCLEASE VII (ENDOVII) FROM PHAGE T4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other ENDOVII N62D MUTANT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.2 HANGING DROP VAPOUR DIFFUSION 1 + 1 UL OF PROTEIN SOLUTION:
16 MG/ML ENDOVII, 175 MM NACL, 20 MM MGCL2, 2 MM ZNCL2,
10 MM 2-MERCAPTO-ETHANOL, 10 % GLYCEROL, 10 MM MOPS PH6.5;
WELL: 16-18% PEG 5000 MME, 200 MM CACL2, 20 MM AMMONIUM SULPHATE,
10 MM 2-MERCAPTO-ETHANOL, 100 MM TRIS PH 8.2, ~ 1 MM SODIUM AZIDE, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.8 57.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.99 α = 90 b = 39.45 β = 106.2 c = 75.75 γ = 90
Symmetry Space Group C 1 2 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 IMAGE PLATE MARRESEARCH NI COATED MIRRORS 1998-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.33 44.281 99.4 0.06 11.8 3.8 17578 36.81
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.33 2.46 99.3 0.253 3 3.7
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-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SIRAS THROUGHOUT ENDOVII N62D MUTANT 2.4 10 15326 15326 828 99.5 0.2395 0.308 RANDOM 46.84
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 p_transverse_tor 32.5 p_staggered_tor 15.2 p_planar_tor 5.5 p_scangle_it 3.301 p_mcangle_it 2.94 p_scbond_it 2.092 p_mcbond_it 1.955 p_multtor_nbd 0.268 p_singtor_nbd 0.177 p_xyhbond_nbd 0.177
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 32.5 p_staggered_tor 15.2 p_planar_tor 5.5 p_scangle_it 3.301 p_mcangle_it 2.94 p_scbond_it 2.092 p_mcbond_it 1.955 p_multtor_nbd 0.268 p_singtor_nbd 0.177 p_xyhbond_nbd 0.177 p_chiral_restr 0.157 p_angle_d 0.032 p_bond_d 0.027 p_planar_d 0.024 p_angle_deg p_hb_or_metal_coord p_plane_restr p_xhyhbond_nbd p_orthonormal_tor p_special_tor
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2544 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 5
Software Software Software Name Purpose XDS data scaling SCALA data scaling SHARP phasing REFMAC refinement XDS data reduction CCP4 data scaling