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crystal structure of the ATPase domain of PAN from Pyrococcus horikoshii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H4M 3H4M, chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 NaCH3COO 0.1 M pH 5.5, NH4PO4 0.6 M
Crystal Properties Matthews coefficient Solvent content 2.37 48.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.344 α = 90 b = 46.488 β = 115.18 c = 56.428 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 PIXEL PSI PILATUS 6M 2014-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9537 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.943 47.946 97.7 0.072 0.081 0.031 9.7 6.8 19463 19463 44.06
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 2.05 93.1 1.248 1.248 0.576 0.6 6.4 2687
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 3H4M, chain A 1.943 47.948 1.33 19447 918 97.36 0.2237 0.223 0.2335 0.2392 0.2478 68.8708
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 20.512 f_angle_d 1.621 f_chiral_restr 0.093 f_bond_d 0.017 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1952 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 39
Software Software Software Name Purpose PHENIX refinement SCALA data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction