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Crystal structure of the Endonuclease V (SAV1684) from Streptomyces avermitilis. Northeast Structural Genomics Consortium Target SvR196
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GA2 PDB entry 3GA2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 291 Protein solution: 10 mM Tris-HCl pH 7.5, 100 mM Sodium chloride, 5 mM DTT. Reservoir solution: 100 mM Bis-Tris pH 7.2, 20% PEG 3350, 200 mM Magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.28 46.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.742 α = 90 b = 40.563 β = 121.61 c = 107.422 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 CCD MAR CCD 165 mm mirrors 2007-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4C 0.97853 NSLS X4C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.6 50 98 0.043 0.044 24.8 2.8 115159 112856 13.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.69 98 0.103 0.1 8.86 2.4 13864
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 3GA2 1.6 19.83 2 2 112856 110428 5494 94 0.179 0.178 0.177 0.1842 0.194 0.2004 RANDOM 16
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] -0.15 0.14 1.36 -1.21
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24 c_angle_deg 1.4 c_improper_angle_d 0.95 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3362 Nucleic Acid Atoms Solvent Atoms 743 Heterogen Atoms 19
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction SCALEPACK data scaling COMO phasing REFMAC refinement