3COV

Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase at 1.5 Ang resolution- apo form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MOPPDB entry 1MOP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829312-14% PEG3000, 100-150 mM Li2SO4, 100 mM imidazole, 2-4% v/v ethanol, 5-10% v/v glycerol and 20 mM MgCl2., pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1943.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.27α = 90
b = 70.92β = 99.16
c = 81.87γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-09-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.973ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.55099.70.0590.05913.13.786748864882.516.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.531000.3410.3413.75725

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 REPLACEMENTTHROUGHOUTPDB entry 1MOP1.547.678265982138432799.370.171070.171070.169780.19547RANDOM19.743
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
r_dihedral_angle_2_deg37.024
r_dihedral_angle_4_deg16.253
r_dihedral_angle_3_deg12.985
r_dihedral_angle_1_deg9.01
r_scangle_it4.508
r_scbond_it3.01
r_mcangle_it2.753
r_mcbond_it1.984
r_angle_refined_deg1.395
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.024
r_dihedral_angle_4_deg16.253
r_dihedral_angle_3_deg12.985
r_dihedral_angle_1_deg9.01
r_scangle_it4.508
r_scbond_it3.01
r_mcangle_it2.753
r_mcbond_it1.984
r_angle_refined_deg1.395
r_nbtor_refined0.307
r_symmetry_vdw_refined0.222
r_nbd_refined0.207
r_symmetry_hbond_refined0.133
r_xyhbond_nbd_refined0.131
r_chiral_restr0.078
r_bond_refined_d0.013
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4150
Nucleic Acid Atoms
Solvent Atoms601
Heterogen Atoms59

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing