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Macrodomain of Thermus aquaticus DarG in complex with ADP-ribose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DX6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 200 mM sodium bromide and 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.51 51.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.41 α = 90 b = 60.392 β = 90 c = 76.706 γ = 90
Symmetry Space Group P 21 21 21
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 DECTRIS PILATUS 2M 2014-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.97625 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.5 60.39 98.2 0.044 25 6.7 6306
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 85.8 0.153 0.992 7 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT 2DX6 2.5 47.45 5955 313 98.03 0.19695 0.1946 0.2007 0.24375 0.2489 RANDOM 51.825
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] -4.64 -3.58 8.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.943 r_dihedral_angle_3_deg 15.917 r_dihedral_angle_4_deg 14.891 r_dihedral_angle_1_deg 6.88 r_long_range_B_other 4.704 r_long_range_B_refined 4.703 r_scangle_other 2.63 r_mcangle_it 2.578 r_mcangle_other 2.577 r_angle_refined_deg 1.603
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.943 r_dihedral_angle_3_deg 15.917 r_dihedral_angle_4_deg 14.891 r_dihedral_angle_1_deg 6.88 r_long_range_B_other 4.704 r_long_range_B_refined 4.703 r_scangle_other 2.63 r_mcangle_it 2.578 r_mcangle_other 2.577 r_angle_refined_deg 1.603 r_scbond_it 1.524 r_scbond_other 1.523 r_mcbond_it 1.512 r_mcbond_other 1.509 r_angle_other_deg 0.99 r_chiral_restr 0.078 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1214 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing