☰ Navigation Tabs
Mycoplasma genitalium DnaK-NBD in complex with AMP-PNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OBW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 Tris-HCl, ammonium sulfate, potassium thiocyanate
Crystal Properties Matthews coefficient Solvent content 3.42 64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.065 α = 90 b = 157.065 β = 90 c = 56.782 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 0.9495 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 1.3 78.73 99.5 0.5 0.3 12 7.6 127585
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 1.3 1.37 97 0.58 0.36 1.9 2
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 5OBW 1.3 78.53 121266 6297 99.49 0.142 0.141 0.1453 0.1614 0.1674 RANDOM 24.423
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] 0.48 0.24 0.48 -1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.862 r_sphericity_free 31.934 r_sphericity_bonded 21.546 r_dihedral_angle_4_deg 13.38 r_dihedral_angle_3_deg 12.894 r_rigid_bond_restr 10.811 r_dihedral_angle_1_deg 4.931 r_angle_other_deg 2.326 r_angle_refined_deg 2.132 r_chiral_restr 0.147
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.862 r_sphericity_free 31.934 r_sphericity_bonded 21.546 r_dihedral_angle_4_deg 13.38 r_dihedral_angle_3_deg 12.894 r_rigid_bond_restr 10.811 r_dihedral_angle_1_deg 4.931 r_angle_other_deg 2.326 r_angle_refined_deg 2.132 r_chiral_restr 0.147 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_gen_planes_other 0.008 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2765 Nucleic Acid Atoms Solvent Atoms 315 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling PHASER phasing