9IMR | pdb_00009imr

Crystal structure of geranylgeranyl pyrophosphate synthase Rv0562 from Mycobacterium tuberculosis in complex with IPP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WV0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP929830% PEG 6000, 0.6 M Bicine, pH 9.0
Crystal Properties
Matthews coefficientSolvent content
2.3647.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.796α = 90
b = 115.643β = 90
c = 119.27γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELBruker PHOTON III2021-08-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1LIQUID ANODEBRUKER METALJET1.34138

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
11.8935.9699.10.040230.77.0454521
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)
11.891.9295.20.13026.753.66

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.8932.7851618269798.90.144190.141560.15520.1930.2037RANDOM16.037
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]
-0.02-0.570.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.39
r_dihedral_angle_4_deg17.84
r_dihedral_angle_3_deg12.587
r_long_range_B_refined5.754
r_long_range_B_other5.754
r_dihedral_angle_1_deg5.333
r_scangle_other3.967
r_scbond_it2.553
r_scbond_other2.553
r_mcangle_it2.064
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.39
r_dihedral_angle_4_deg17.84
r_dihedral_angle_3_deg12.587
r_long_range_B_refined5.754
r_long_range_B_other5.754
r_dihedral_angle_1_deg5.333
r_scangle_other3.967
r_scbond_it2.553
r_scbond_other2.553
r_mcangle_it2.064
r_mcangle_other2.064
r_angle_refined_deg1.647
r_angle_other_deg1.492
r_mcbond_it1.41
r_mcbond_other1.41
r_chiral_restr0.088
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4926
Nucleic Acid Atoms
Solvent Atoms919
Heterogen Atoms113

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata scaling
SAINTdata reduction
PHASERphasing