5UN0

Crystal Structure of Mycobacterium Tuberculosis Proteasome-assembly chaperone homologue Rv2125


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MNF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52930.1 M sodium chloride, 0.1 M HEPES pH 7.5, 1.6 M ammonium sulfate, 1% w/v ANAPOE-20, and 2% w/v benzamidine hydrochloride
Crystal Properties
Matthews coefficientSolvent content
2.8957.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 138.25α = 90
b = 79.76β = 103.57
c = 89.03γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152014-07-01MSINGLE WAVELENGTH
21x-ray100CCDADSC QUANTUM 3152014-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X251.1NSLSX25
2SYNCHROTRONNSLS BEAMLINE X29A1.1NSLSX29A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
1330.6598.95.73.618826

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 REPLACEMENTTHROUGHOUT3mnf330.651788195198.830.239050.236430.28914RANDOM40.831
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]
-0.130.37-0.410.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.463
r_dihedral_angle_4_deg20.146
r_dihedral_angle_3_deg18.889
r_long_range_B_refined8.941
r_long_range_B_other8.934
r_dihedral_angle_1_deg7.304
r_scangle_other4.98
r_mcangle_it3.855
r_mcangle_other3.855
r_angle_other_deg3.694
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.463
r_dihedral_angle_4_deg20.146
r_dihedral_angle_3_deg18.889
r_long_range_B_refined8.941
r_long_range_B_other8.934
r_dihedral_angle_1_deg7.304
r_scangle_other4.98
r_mcangle_it3.855
r_mcangle_other3.855
r_angle_other_deg3.694
r_scbond_it3.19
r_scbond_other3.189
r_mcbond_it2.221
r_mcbond_other2.217
r_angle_refined_deg1.381
r_chiral_restr0.079
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_gen_planes_other0.005
r_bond_other_d
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 Atoms5430
Nucleic Acid Atoms
Solvent Atoms86
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing