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Crystal structure of ClpB NBD1 in complex with guanidinium chloride and ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QVR PDB entry 1QVR residues 141-534
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1 M Tris/HCl pH 7.5, 1.0 M LiCl, 18 (w/v) % PEG 6000, 10 mM MgCl2, 10 mM GdmCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.55 51.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.99 α = 90 b = 60.99 β = 90 c = 213.87 γ = 120
Symmetry Space Group P 31 2 1
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 PSI PILATUS 6M 2012-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9785 SLS X10SA
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 2.2 50 99.4 0.054 19.5 4.9 24236 24236 39.9
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 2.2 2.3 99.1 0.391 4.8 5.2 2926
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 (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 PDB entry 1QVR residues 141-534 2.2 47.36 23027 23027 1207 100 0.22742 0.22536 0.2305 0.26631 0.2665 RANDOM 43.543
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] 0.79 0.39 0.79 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.102 r_dihedral_angle_4_deg 16.866 r_dihedral_angle_3_deg 16.011 r_dihedral_angle_1_deg 4.79 r_scangle_it 2.95 r_scbond_it 1.66 r_angle_refined_deg 1.189 r_mcangle_it 0.923 r_mcbond_it 0.459 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.102 r_dihedral_angle_4_deg 16.866 r_dihedral_angle_3_deg 16.011 r_dihedral_angle_1_deg 4.79 r_scangle_it 2.95 r_scbond_it 1.66 r_angle_refined_deg 1.189 r_mcangle_it 0.923 r_mcbond_it 0.459 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2946 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 32
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XDS data scaling