2Q3D

2.2 A Resolution Crystal Structure of O-Acetylserine Sulfhydrylase (OASS) From MYCOBACTERIUM TUBERCULOSIS in Complex with the Reaction Intermediate ALPHA-AMINOACRYLATE


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Q3BPDB entry 2Q3B, Holoenzyme

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.22930.1 M HEPES, 80% MPD. SOAKED WITH 1 mM O-ACETYL-SERINE FOR 30 MINUTES BEFORE FREEZING., pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.665.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.785α = 90
b = 71.785β = 90
c = 181.179γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMAR CCD 165 mmFirst mirror: Water-cooled vertically collimating cylindrical mirror (R = 7300 m). Second mirror: Toroid mirror for horizontal and vertical focusing (R=3300m, R=27mm).2006-10-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-31.000MAX III911-3

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
12.271.898.90.09114.25.4246072460743
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)
12.22.3299.80.4992.45.33550

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, Holoenzyme2.228.352328723287124598.490.196410.196410.193790.24943RANDOM30.42
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]
3.563.56-7.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.28
r_dihedral_angle_3_deg16.682
r_dihedral_angle_4_deg14.801
r_dihedral_angle_1_deg5.487
r_scangle_it2.668
r_scbond_it1.739
r_angle_refined_deg1.419
r_mcangle_it0.97
r_mcbond_it0.581
r_xyhbond_nbd_refined0.508
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.28
r_dihedral_angle_3_deg16.682
r_dihedral_angle_4_deg14.801
r_dihedral_angle_1_deg5.487
r_scangle_it2.668
r_scbond_it1.739
r_angle_refined_deg1.419
r_mcangle_it0.97
r_mcbond_it0.581
r_xyhbond_nbd_refined0.508
r_nbtor_refined0.31
r_symmetry_vdw_refined0.233
r_symmetry_hbond_refined0.221
r_nbd_refined0.211
r_chiral_restr0.092
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2271
Nucleic Acid Atoms
Solvent Atoms42
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
MARCCD-mxCubedata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing