3IFT

Crystal structure of glycine cleavage system protein H from Mycobacterium tuberculosis, using X-rays from the Compact Light Source.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.32901.5M SODIUM CITRATE, 50MM BISTRIS PH 6.3; MYTUD.01046.A AT 27MG/ML, , VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthew coefficientSolvent content
2.3547

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.45α = 90
b = 51.01β = 95.1
c = 32.57γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2009-07-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONOTHER0.81836

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
122098.80.09510.173.195359535-321.39
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)
22.0599.30.3853.23.1710

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 3hgb2209535953545998.90.1850.1810.253RANDOM12.01
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]
-0.10.210.76-0.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.103
r_dihedral_angle_4_deg24.186
r_dihedral_angle_3_deg11.988
r_dihedral_angle_1_deg7.182
r_scangle_it3.677
r_scbond_it2.352
r_mcangle_it1.668
r_angle_refined_deg1.586
r_mcbond_it0.919
r_angle_other_deg0.858
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.103
r_dihedral_angle_4_deg24.186
r_dihedral_angle_3_deg11.988
r_dihedral_angle_1_deg7.182
r_scangle_it3.677
r_scbond_it2.352
r_mcangle_it1.668
r_angle_refined_deg1.586
r_mcbond_it0.919
r_angle_other_deg0.858
r_mcbond_other0.211
r_chiral_restr0.076
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_sphericity_bonded
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_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_rigid_bond_restr
r_sphericity_free
r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms999
Nucleic Acid Atoms
Solvent Atoms161
Heterogen Atoms

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling