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Crystal structure of aprataxin ortholog Hnt3 in complex with DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SP4 PDB ENTRY 3SP4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 1.6M Ammonium Sulfate, 0.1M HEPES, pH7.5
, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.77 55.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 220.409 α = 90 b = 220.409 β = 90 c = 135.031 γ = 120
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 2010-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9791 SSRF BL17U
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 1.91 50 99.5 0.08 0.08 32.6 9.8 96371 96371 28
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 1.91 1.98 95 0.481 0.481 4.1 8.1 9158
Refinement Statistics Diffraction ID Structure Solution 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 (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 PDB ENTRY 3SP4 1.912 23.496 0.12 0.12 91580 91549 4616 94.91 0.1765 0.1746 0.18 0.2115 0.214 RANDOM 27.2893
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] -0.0371 -0.0371 0.0742
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 19.559 f_angle_d 1.085 f_chiral_restr 0.067 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6516 Nucleic Acid Atoms 1138 Solvent Atoms 1105 Heterogen Atoms 84
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling