2Q3C

2.1 A Resolution Crystal Structure of O-Acetylserine Sulfhydrylase (OASS) Holoenzyme From MYCOBACTERIUM TUBERCULOSIS in Complex with the Inhibitory Peptide DFSI


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Q3Bpdb entry 2Q3B, Holoenzyme

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82930.1 M HEPES, 80% MPD, 4 mM DFSI-peptide, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.6165.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.458α = 90
b = 72.458β = 90
c = 178.936γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 2102007-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.934ESRFID14-1

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
12.159.6693.20.08911.55.1265712657131
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)
12.12.2196.20.3523.353941

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 2Q3B, Holoenzyme2.151.232517125171134192.280.188260.188260.187230.20747RANDOM36.734
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]
1.941.94-3.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.041
r_dihedral_angle_4_deg16.614
r_dihedral_angle_3_deg12.736
r_angle_other_deg6.9
r_dihedral_angle_1_deg4.835
r_scangle_it2.818
r_scbond_it1.588
r_angle_refined_deg1.195
r_mcangle_it1.002
r_mcbond_it0.587
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.041
r_dihedral_angle_4_deg16.614
r_dihedral_angle_3_deg12.736
r_angle_other_deg6.9
r_dihedral_angle_1_deg4.835
r_scangle_it2.818
r_scbond_it1.588
r_angle_refined_deg1.195
r_mcangle_it1.002
r_mcbond_it0.587
r_nbtor_refined0.299
r_symmetry_vdw_refined0.216
r_nbd_refined0.192
r_xyhbond_nbd_refined0.14
r_chiral_restr0.13
r_symmetry_hbond_refined0.109
r_nbd_other0.093
r_nbtor_other0.047
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2276
Nucleic Acid Atoms
Solvent Atoms163
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing