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Mycoplasma genitalium DnaK-NBD
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 293 Tris-HCl, ammonium sulfate, potassium thiocyanate
Crystal Properties Matthews coefficient Solvent content 3.86 68.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.921 α = 90 b = 157.921 β = 90 c = 64.697 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 1.78 78.96 99.4 0.03 0.02 16 4.8 57432
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 1.78 1.83 98 0.51 0.36 1.7 2.3
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 1.78 45 54515 2915 99.37 0.18275 0.18162 0.1918 0.20369 0.2162 RANDOM 42.161
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] 0.63 0.31 0.63 -2.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.752 r_dihedral_angle_3_deg 13.323 r_dihedral_angle_4_deg 10.782 r_long_range_B_other 8.735 r_long_range_B_refined 8.713 r_dihedral_angle_1_deg 5.407 r_scangle_other 5.136 r_scbond_other 3.433 r_scbond_it 3.432 r_mcangle_other 2.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.752 r_dihedral_angle_3_deg 13.323 r_dihedral_angle_4_deg 10.782 r_long_range_B_other 8.735 r_long_range_B_refined 8.713 r_dihedral_angle_1_deg 5.407 r_scangle_other 5.136 r_scbond_other 3.433 r_scbond_it 3.432 r_mcangle_other 2.6 r_mcangle_it 2.599 r_mcbond_it 1.741 r_mcbond_other 1.737 r_angle_refined_deg 1.484 r_angle_other_deg 0.927 r_chiral_restr 0.09 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 2821 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling PHASER phasing