1ZYU

Crystal structure of Mycobacterium tuberculosis shikimate kinase in complex with shikimate and amppcp at 2.85 angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1L4U 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5292PEG 3000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.8755.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.954α = 90
b = 59.954β = 90
c = 102.666γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER PROTEUM 300mirror2005-04-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.000APS22-ID

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
12.8528.78860.1289.24.14580458036.9
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)
2.853.0344.70.3031.72.1

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 REPLACEMENTTHROUGHOUT1L4U2.928.784580448847288.70.19810.19810.1980.251RANDOM48.7
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]
10.0114.2510.01-20.03
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.9
c_scangle_it9.24
c_scbond_it5.96
c_mcangle_it5.48
c_mcbond_it3.43
c_angle_deg1.1
c_improper_angle_d0.83
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.9
c_scangle_it9.24
c_scbond_it5.96
c_mcangle_it5.48
c_mcbond_it3.43
c_angle_deg1.1
c_improper_angle_d0.83
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1253
Nucleic Acid Atoms
Solvent Atoms48
Heterogen Atoms43

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement