7NDX

Crystal structure of the human HSP40 DNAJB1-CTDs in complex with a peptide of NudC


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP42980.1 M of sodium acetate trihydrate and 15% (v/v) of polyethylene glycol 400
Crystal Properties
Matthews coefficientSolvent content
3.564.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.3α = 90
b = 128.264β = 90
c = 135.213γ = 90
Symmetry
Space GroupI 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray193PIXELDECTRIS PILATUS 2M-F2020-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.0SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
12.5446.5399.90.140.9916.51312295
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.542.650.66

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3AGY2.54146.531229560799.9110.2350.23280.268169.028
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]
-3.9142.6071.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.139
r_dihedral_angle_4_deg21.374
r_dihedral_angle_3_deg18.674
r_dihedral_angle_1_deg8.467
r_lrange_it5.915
r_lrange_other5.914
r_scangle_it3.895
r_scangle_other3.895
r_mcangle_it3.57
r_mcangle_other3.568
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.139
r_dihedral_angle_4_deg21.374
r_dihedral_angle_3_deg18.674
r_dihedral_angle_1_deg8.467
r_lrange_it5.915
r_lrange_other5.914
r_scangle_it3.895
r_scangle_other3.895
r_mcangle_it3.57
r_mcangle_other3.568
r_scbond_it2.4
r_scbond_other2.399
r_mcbond_it2.247
r_mcbond_other2.243
r_angle_refined_deg1.799
r_angle_other_deg1.154
r_nbd_refined0.206
r_nbd_other0.201
r_symmetry_nbd_other0.187
r_symmetry_nbd_refined0.173
r_nbtor_refined0.158
r_xyhbond_nbd_refined0.137
r_symmetry_xyhbond_nbd_refined0.129
r_symmetry_nbtor_other0.078
r_chiral_restr0.065
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1430
Nucleic Acid Atoms
Solvent Atoms22
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing