3DKI

2.1 A X-ray structure of CysM (Rv1336) from Mycobacterium tuberculosis an O-phosphoserine dependent cysteine synthase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52930.1M Tris-HCl pH 7.5, 0.1M K2HPO4, 4.3M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3547.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.423α = 90
b = 89.222β = 90
c = 98.766γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 315Channel cut ESRF monochromator, Torodial focusing mirror2008-02-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.93400ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.15098.80.0710.08513.93.138897384312.631.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.2199.70.4530.5392.63.25613

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)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 2Q3B2.128.582.63713636490189898.260.1910.193430.190880.24147RANDOM23.102
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]
0.27-1.10.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.112
r_dihedral_angle_3_deg15.845
r_dihedral_angle_4_deg14.248
r_dihedral_angle_1_deg5.851
r_scangle_it3.236
r_scbond_it2.029
r_angle_refined_deg1.398
r_mcangle_it1.275
r_angle_other_deg0.957
r_mcbond_it0.682
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.112
r_dihedral_angle_3_deg15.845
r_dihedral_angle_4_deg14.248
r_dihedral_angle_1_deg5.851
r_scangle_it3.236
r_scbond_it2.029
r_angle_refined_deg1.398
r_mcangle_it1.275
r_angle_other_deg0.957
r_mcbond_it0.682
r_symmetry_hbond_refined0.315
r_symmetry_vdw_other0.28
r_symmetry_vdw_refined0.268
r_nbd_refined0.213
r_nbd_other0.2
r_xyhbond_nbd_refined0.189
r_nbtor_refined0.172
r_mcbond_other0.138
r_nbtor_other0.086
r_metal_ion_refined0.086
r_chiral_restr0.083
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4567
Nucleic Acid Atoms
Solvent Atoms219
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
MxCuBEdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing