9KUQ | pdb_00009kuq

Crystal structure of a C45 isoprenyl diphosphate synthase, Rv0562 from Mycobacterium tuberculosis


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529830% PEG 6000, 0.6 M Bicine, pH 9.0
Crystal Properties
Matthews coefficientSolvent content
2.3146.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.192α = 90
b = 84.192β = 90
c = 80.549γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2024-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE TPS 05A1.0NSRRCTPS 05A

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
11.732599.90.04842.219.921428
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)
11.731.790.7232.58

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 REPLACEMENTTHROUGHOUT222.6521428115499.520.230350.226830.23490.293650.2993RANDOM51.989
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]
0.280.140.28-0.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.614
r_dihedral_angle_3_deg16.98
r_dihedral_angle_4_deg14.427
r_long_range_B_other9.865
r_long_range_B_refined9.859
r_scangle_other7.733
r_mcangle_other6.867
r_mcangle_it6.859
r_dihedral_angle_1_deg6.192
r_scbond_it5.502
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.614
r_dihedral_angle_3_deg16.98
r_dihedral_angle_4_deg14.427
r_long_range_B_other9.865
r_long_range_B_refined9.859
r_scangle_other7.733
r_mcangle_other6.867
r_mcangle_it6.859
r_dihedral_angle_1_deg6.192
r_scbond_it5.502
r_scbond_other5.5
r_mcbond_it5.319
r_mcbond_other5.297
r_angle_refined_deg1.641
r_angle_other_deg1.323
r_chiral_restr0.082
r_bond_refined_d0.01
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 Atoms2307
Nucleic Acid Atoms
Solvent Atoms149
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata scaling
SAINTdata reduction
PHASERphasing