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ClpB NBD2 from T. thermophilus in complex with ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QVR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.2M sodium citrate, 0.1M HEPES/NaOH, 20% isopropanol, 2mM ADP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.62 53.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.06 α = 90 b = 76.06 β = 90 c = 120.54 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 CCD ADSC QUANTUM 4 2003-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 1.01096 ESRF ID14-4
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 2.3 20 98.4 0.085 10.12 17302 17302 -3 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.4 98.6 0.774 2.12
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1QVR 2.4 19.27 14464 14464 762 99.98 0.23706 0.23706 0.23522 0.2362 0.27211 0.2675 RANDOM 65.332
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] 0.75 0.38 0.75 -1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.507 r_dihedral_angle_4_deg 15.924 r_dihedral_angle_3_deg 15.509 r_dihedral_angle_1_deg 4.3 r_angle_refined_deg 0.922 r_angle_other_deg 0.719 r_scangle_it 0.603 r_scbond_it 0.363 r_mcangle_it 0.192 r_mcbond_it 0.172
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.507 r_dihedral_angle_4_deg 15.924 r_dihedral_angle_3_deg 15.509 r_dihedral_angle_1_deg 4.3 r_angle_refined_deg 0.922 r_angle_other_deg 0.719 r_scangle_it 0.603 r_scbond_it 0.363 r_mcangle_it 0.192 r_mcbond_it 0.172 r_nbd_refined 0.16 r_nbtor_refined 0.159 r_nbd_other 0.151 r_symmetry_hbond_refined 0.138 r_symmetry_vdw_other 0.136 r_xyhbond_nbd_refined 0.087 r_symmetry_vdw_refined 0.081 r_nbtor_other 0.078 r_chiral_restr 0.048 r_mcbond_other 0.021 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2535 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 27
Software Software Software Name Purpose ADSC data collection CNS refinement REFMAC refinement XDS data reduction XSCALE data scaling CNS phasing