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Crystal structure of N-terminal domain of Human SIRT7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ANF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 0.1M Sodium cacodylate, pH 5.5, 25% w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.05 40.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.49 α = 90 b = 49.33 β = 101.2 c = 65.68 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 MARMOSAIC 225 mm CCD 2015-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE BL-21 0.97947 RRCAT INDUS-2 BL-21
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 2.334 64.429 98.8 0.112 8.1 3.7 16201 26.41
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 2.334 2.46 96.4 0.391 1.9 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1ANF 2.334 48.605 1.36 16177 820 98.74 0.1856 0.183 0.1864 0.2368 0.2348 33.0914
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 f_dihedral_angle_d 14.421 f_angle_d 0.644 f_chiral_restr 0.024 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3318 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 23
Software Software Software Name Purpose PHENIX refinement MOSFLM data processing SCALA data scaling PHASER phasing PDB_EXTRACT data extraction Coot model building iMOSFLM data reduction