5GKM

Crystal structure of the N-terminal Domain of Caseinolytic protease associated chaperone ClpD from Arabidopsis thaliana


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5CTZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP629120%(v/v) 2-propanol, 20%(w/v) PEG MME 2000, 100 mM MES monohydrate
Crystal Properties
Matthews coefficientSolvent content
238.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.08α = 90
b = 37.31β = 96.08
c = 99.98γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2016-04-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.9537ESRFBM14

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
11.6501000.0650.9959.84.237033
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.631000.5830.71724.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5CTZ1.6353549717711000.1970.1960.212RANDOM23.11
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]
0.330.050.34-0.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.456
r_dihedral_angle_4_deg22.165
r_dihedral_angle_3_deg12.341
r_dihedral_angle_1_deg5.749
r_long_range_B_refined4.851
r_long_range_B_other4.835
r_scangle_other4.089
r_scbond_it2.961
r_scbond_other2.96
r_mcangle_it2.042
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.456
r_dihedral_angle_4_deg22.165
r_dihedral_angle_3_deg12.341
r_dihedral_angle_1_deg5.749
r_long_range_B_refined4.851
r_long_range_B_other4.835
r_scangle_other4.089
r_scbond_it2.961
r_scbond_other2.96
r_mcangle_it2.042
r_mcangle_other2.041
r_angle_refined_deg1.706
r_mcbond_it1.584
r_mcbond_other1.579
r_angle_other_deg0.886
r_chiral_restr0.118
r_bond_refined_d0.018
r_gen_planes_refined0.016
r_bond_other_d0.006
r_gen_planes_other0.003
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 AtomsNumber
Protein Atoms2301
Nucleic Acid Atoms
Solvent Atoms120
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing
Aimlessdata scaling
iMOSFLMdata reduction