2Y88

CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PHOSPHORIBOSYL ISOMERASE (VARIANT D11N) WITH BOUND PRFAR


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Y85PDB ENTRY 2Y85

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.1M HEPES PH7.5, 1.4M TRI-SODIUM CITRATE
Crystal Properties
Matthews coefficientSolvent content
2.5652.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.27α = 90
b = 63.27β = 90
c = 131.22γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2006-02-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X13EMBL/DESY, HAMBURGX13

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
11.332099.10.040.588.461458-316.9
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)
11.331.495.80.583.47.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2Y851.3356.9858387308299.7090.140.13790.1836RANDOM14.109
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]
0.1090.109-0.218
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.422
r_dihedral_angle_4_deg19.898
r_dihedral_angle_3_deg11.95
r_scangle_it7.261
r_dihedral_angle_1_deg6.24
r_scbond_it6.054
r_mcangle_it5.129
r_mcbond_it4.75
r_angle_refined_deg2.206
r_angle_other_deg1.183
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.422
r_dihedral_angle_4_deg19.898
r_dihedral_angle_3_deg11.95
r_scangle_it7.261
r_dihedral_angle_1_deg6.24
r_scbond_it6.054
r_mcangle_it5.129
r_mcbond_it4.75
r_angle_refined_deg2.206
r_angle_other_deg1.183
r_symmetry_vdw_other0.344
r_nbd_refined0.242
r_nbd_other0.236
r_xyhbond_nbd_refined0.197
r_symmetry_hbond_refined0.195
r_nbtor_refined0.191
r_symmetry_vdw_refined0.187
r_chiral_restr0.161
r_nbtor_other0.116
r_bond_refined_d0.025
r_gen_planes_refined0.011
r_bond_other_d0.003
r_gen_planes_other0.002
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1804
Nucleic Acid Atoms
Solvent Atoms394
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing