4HSE

Crystal structure of ClpB NBD1 in complex with guanidinium chloride and ADP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QVRPDB entry 1QVR residues 141-534

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.1 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 coefficientSolvent content
2.5551.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.99α = 90
b = 60.99β = 90
c = 213.87γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2012-06-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.9785SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.25099.40.05419.54.9242362423639.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.399.10.3914.85.22926

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1QVR residues 141-5342.247.36230272302712071000.227420.225360.26631RANDOM43.543
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]
0.790.390.79-1.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.102
r_dihedral_angle_4_deg16.866
r_dihedral_angle_3_deg16.011
r_dihedral_angle_1_deg4.79
r_scangle_it2.95
r_scbond_it1.66
r_angle_refined_deg1.189
r_mcangle_it0.923
r_mcbond_it0.459
r_chiral_restr0.078
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.102
r_dihedral_angle_4_deg16.866
r_dihedral_angle_3_deg16.011
r_dihedral_angle_1_deg4.79
r_scangle_it2.95
r_scbond_it1.66
r_angle_refined_deg1.189
r_mcangle_it0.923
r_mcbond_it0.459
r_chiral_restr0.078
r_bond_refined_d0.009
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2946
Nucleic Acid Atoms
Solvent Atoms86
Heterogen Atoms32

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling