2A15

X-ray Crystal Structure of RV0760 from Mycobacterium Tuberculosis at 1.68 Angstrom Resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherthe model was obtained from a SAD solution from the data collected on SeMet variant of the same protein.

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52971.6 M Na, K Phosphate, 100mM Hepes buffer pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
2.6553.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.6α = 90
b = 55.6β = 90
c = 104.74γ = 120
Symmetry
Space GroupP 32 1 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-04-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.1ALS8.3.1

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
11.6848.1799.72139921399
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.681.7499.37.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTthe model was obtained from a SAD solution from the data collected on SeMet variant of the same protein.1.6848.172032020320107699.740.1780.1780.1760.207RANDOM21.639
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]
0.540.270.54-0.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.741
r_dihedral_angle_4_deg17.906
r_dihedral_angle_3_deg11.827
r_scangle_it9.11
r_scbond_it6.551
r_dihedral_angle_1_deg6.462
r_mcangle_it4.043
r_mcbond_it3.025
r_angle_refined_deg1.571
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.741
r_dihedral_angle_4_deg17.906
r_dihedral_angle_3_deg11.827
r_scangle_it9.11
r_scbond_it6.551
r_dihedral_angle_1_deg6.462
r_mcangle_it4.043
r_mcbond_it3.025
r_angle_refined_deg1.571
r_nbtor_refined0.312
r_nbd_refined0.208
r_symmetry_vdw_refined0.163
r_symmetry_hbond_refined0.161
r_xyhbond_nbd_refined0.158
r_chiral_restr0.135
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1059
Nucleic Acid Atoms
Solvent Atoms190
Heterogen Atoms9

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
MOLREPphasing
ELVESrefinement
ELVESdata reduction