2VZZ

Crystal structure of Rv0802c from Mycobacterium tuberculosis in Complex with Succinyl-CoA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VZYPDB ENTRY 2VZY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17PROTEIN AT 8 MG/ML IN 20 MM TEA PH 8.5, 100 MM AMMONIUM SULFATE, 1 MM EDTA, 1 MM DTT, 2 MM COA, 4 MM SUCCOA CRYSTALLIZED IN 1 M LICL, 100 MM HEPES PH 7.0. CRYOPROTECTED IN PRECIPITANT SOLUTION PLUS 20 MM SUCCOA AND 20% GLYCEROL
Crystal Properties
Matthews coefficientSolvent content
3.0354

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.165α = 90
b = 135.172β = 90
c = 164.077γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93IMAGE PLATERIGAKU IMAGE PLATEOSMIC BLUE CONFOCAL2004-03-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R

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
12.310495.90.0615.33.553759
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)
12.32.3892.80.24.83

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 2VZY2.3104.2651029273095.80.1720.1690.222RANDOM19.81
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]
0.331.26-1.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.199
r_dihedral_angle_4_deg16.542
r_dihedral_angle_3_deg14.568
r_dihedral_angle_1_deg5.914
r_scangle_it3.623
r_scbond_it2.247
r_angle_refined_deg1.684
r_mcangle_it1.321
r_mcbond_it0.779
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.199
r_dihedral_angle_4_deg16.542
r_dihedral_angle_3_deg14.568
r_dihedral_angle_1_deg5.914
r_scangle_it3.623
r_scbond_it2.247
r_angle_refined_deg1.684
r_mcangle_it1.321
r_mcbond_it0.779
r_nbtor_refined0.304
r_nbd_refined0.204
r_symmetry_vdw_refined0.188
r_symmetry_hbond_refined0.155
r_xyhbond_nbd_refined0.141
r_chiral_restr0.103
r_bond_refined_d0.015
r_gen_planes_refined0.006
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 Atoms6763
Nucleic Acid Atoms
Solvent Atoms413
Heterogen Atoms220

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing