4WSP

Racemic crystal structure of Rv1738 from Mycobacterium tuberculosis (Form-I)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4WPY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52921 microlitre of protein solution containing 9 mg/ml L-Rv1738 and 9 mg/ml D-Rv1738 in water was mixed with 1 microlitre of well solution containing 0.1 M BIS-TRIS pH 5.5, 0.2 M NaCl, 25 % (w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
1.6626

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.13α = 90
b = 32.401β = 125.06
c = 58.214γ = 90
Symmetry
Space GroupC 1 2/c 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2008-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-BM-B0.97934APS23-BM-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
11.6547.6598.10.0570.0410.9989.42.81758449.07
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.6896.60.8460.5970.86912.8842

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4WPY1.6539.3441.3416914123997.760.25110.250.2644Random selection49.4724
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.454
f_angle_d1.067
f_chiral_restr0.056
f_bond_d0.009
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms621
Nucleic Acid Atoms
Solvent Atoms18
Heterogen Atoms1

Software

Software
Software NamePurpose
Aimlessdata scaling
XDSdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction