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Mycoplasma genitalium DnaK-NBD in complex with ATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OBU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Tris-HCl, ammonium sulfate, potassium thiocyanate
Crystal Properties Matthews coefficient Solvent content 3.43 64.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.916 α = 90 b = 157.916 β = 90 c = 57.504 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 PIXEL DECTRIS PILATUS3 6M 2014-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9795 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.4 78.96 99.1 0.057 0.028 11.3 5.5 98799
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.44 92 0.069 0.032 1.5 1.8
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 5OBU 1.4 78.96 98799 5160 99.1 0.177 0.1759 0.177 0.1973 0.1986 RANDOM 23.13
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] 1.18 0.59 1.18 -3.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.804 r_sphericity_free 32.016 r_sphericity_bonded 16.571 r_dihedral_angle_4_deg 12.364 r_dihedral_angle_3_deg 10.941 r_dihedral_angle_1_deg 5.507 r_angle_refined_deg 1.449 r_rigid_bond_restr 1.43 r_angle_other_deg 0.91 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.804 r_sphericity_free 32.016 r_sphericity_bonded 16.571 r_dihedral_angle_4_deg 12.364 r_dihedral_angle_3_deg 10.941 r_dihedral_angle_1_deg 5.507 r_angle_refined_deg 1.449 r_rigid_bond_restr 1.43 r_angle_other_deg 0.91 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2822 Nucleic Acid Atoms Solvent Atoms 381 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling PHASER phasing