2CBY

Crystal structure of the ATP-dependent Clp Protease proteolytic subunit 1 (ClpP1) from Mycobacterium tuberculosis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8THE PROTEIN WAS CRYSTALLISED BY THE VAPOUR DIFFUSION METHOD IN HANGING DROPS CONTAINING A 1:1 MIXTURE OF 3 MG/ML PROTEIN SOLUTION (IN 50 MM TRIS-HCL PH 8) AND RESERVOIR SOLUTION INCLUDING 1 M AMMONIUM SULPHATE IN 0.1 M HEPES PH 8.
Crystal Properties
Matthews coefficientSolvent content
3.8367.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 178.255α = 90
b = 178.255β = 90
c = 264.914γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARRESEARCH2001-08-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-3ESRFID14-3

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
12.676.71000.1624.322.27672840.12
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)
12.62.741000.696.622.5

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1TYF2.6154.37664738951000.1940.1920.229RANDOM19.59
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]
0.8720.4360.872-1.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.912
r_dihedral_angle_3_deg19.468
r_dihedral_angle_4_deg18.233
r_dihedral_angle_1_deg6.21
r_scangle_it3.798
r_scbond_it2.318
r_angle_refined_deg1.48
r_mcangle_it1.333
r_mcbond_it0.805
r_nbtor_refined0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.912
r_dihedral_angle_3_deg19.468
r_dihedral_angle_4_deg18.233
r_dihedral_angle_1_deg6.21
r_scangle_it3.798
r_scbond_it2.318
r_angle_refined_deg1.48
r_mcangle_it1.333
r_mcbond_it0.805
r_nbtor_refined0.313
r_nbd_refined0.216
r_symmetry_vdw_refined0.193
r_symmetry_hbond_refined0.188
r_xyhbond_nbd_refined0.125
r_chiral_restr0.102
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9149
Nucleic Acid Atoms
Solvent Atoms301
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing