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Crystal structure of the HEPN domain from human sacsin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 295 7% (w/v) PEG 3350, 0.2 M sodium malonate, 0.1 M Bis-Tris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.37 48.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.581 α = 90 b = 72.581 β = 90 c = 201.18 γ = 120
Symmetry Space Group P 32 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 ADSC QUANTUM 210 2009-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.9780 CHESS A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.9 50 98.1 46702 45815 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 86.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.9 45.86 1 46702 45815 2441 98.1 0.186 0.184 0.225 0.2347 RANDOM 29.09
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] -0.16 -0.08 -0.16 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.617 r_dihedral_angle_4_deg 22.062 r_dihedral_angle_3_deg 15.749 r_dihedral_angle_1_deg 5.144 r_scangle_it 3.235 r_scbond_it 2.131 r_angle_refined_deg 1.422 r_mcangle_it 1.276 r_mcbond_it 0.815 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.617 r_dihedral_angle_4_deg 22.062 r_dihedral_angle_3_deg 15.749 r_dihedral_angle_1_deg 5.144 r_scangle_it 3.235 r_scbond_it 2.131 r_angle_refined_deg 1.422 r_mcangle_it 1.276 r_mcbond_it 0.815 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.223 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.198 r_symmetry_hbond_refined 0.16 r_chiral_restr 0.1 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4382 Nucleic Acid Atoms Solvent Atoms 407 Heterogen Atoms 21
Software Software Software Name Purpose ADSC data collection SHELXS phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling