7DNQ

Crystal structure of M.tuberculosis imidazole glycerol phosphate dehydratase in complex with an inhibitor


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP929320% PEG 1500, 0.2M sodium citrate tribasic dehydrate, 0.1M Tris HCL, pH 9.0
Crystal Properties
Matthews coefficientSolvent content
2.4850.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.1α = 90
b = 112.1β = 90
c = 112.1γ = 90
Symmetry
Space GroupP 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2020-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.54178

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.283599.90.9421.5829.311541
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.282.360.66

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4GQU2.2828.0411154158799.8180.1620.15910.209928.777
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_deg35.285
r_dihedral_angle_3_deg16.027
r_dihedral_angle_4_deg13.944
r_dihedral_angle_1_deg7.34
r_lrange_it5.774
r_lrange_other5.731
r_scangle_it4.379
r_scangle_other4.377
r_mcangle_it3.091
r_mcangle_other3.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.285
r_dihedral_angle_3_deg16.027
r_dihedral_angle_4_deg13.944
r_dihedral_angle_1_deg7.34
r_lrange_it5.774
r_lrange_other5.731
r_scangle_it4.379
r_scangle_other4.377
r_mcangle_it3.091
r_mcangle_other3.09
r_scbond_it2.826
r_scbond_other2.824
r_mcbond_it2.026
r_mcbond_other2.022
r_angle_refined_deg1.538
r_angle_other_deg1.325
r_nbd_other0.223
r_symmetry_nbd_refined0.197
r_symmetry_nbd_other0.195
r_nbd_refined0.191
r_symmetry_xyhbond_nbd_refined0.17
r_nbtor_refined0.153
r_xyhbond_nbd_refined0.151
r_symmetry_xyhbond_nbd_other0.091
r_symmetry_nbtor_other0.082
r_chiral_restr0.069
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1459
Nucleic Acid Atoms
Solvent Atoms107
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing