3H7F

Crystal structure of serine hydroxymethyltransferase from Mycobacterium tuberculosis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DKJpdb entry 2dkj modified by ccp4 program chainsaw

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5290HAMPTON INDEX, G12: 25% PEG 3350, 200MM MGCL2, 100MM HEPES, MYTUD.00783.A AT 20 MG/ML, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.1542.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.73α = 90
b = 102.01β = 90
c = 132.12γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rSingle crystal, cylindrically bent, Si(220)2009-04-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.3ALS5.0.3

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
11.580.7499.30.0613.555130938130938-324.67
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)
11.51.5498.90.4632.43.59515

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 2dkj modified by ccp4 program chainsaw1.520130877130877660699.30.1660.1660.1650.196RANDOM16.21
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]
-0.06-1.121.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.072
r_dihedral_angle_4_deg15.58
r_dihedral_angle_3_deg12.112
r_dihedral_angle_1_deg5.965
r_scangle_it3.421
r_scbond_it2.177
r_angle_refined_deg1.629
r_mcangle_it1.334
r_angle_other_deg1.168
r_mcbond_it0.803
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.072
r_dihedral_angle_4_deg15.58
r_dihedral_angle_3_deg12.112
r_dihedral_angle_1_deg5.965
r_scangle_it3.421
r_scbond_it2.177
r_angle_refined_deg1.629
r_mcangle_it1.334
r_angle_other_deg1.168
r_mcbond_it0.803
r_mcbond_other0.245
r_chiral_restr0.101
r_bond_refined_d0.023
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6238
Nucleic Acid Atoms
Solvent Atoms962
Heterogen Atoms1

Software

Software
Software NamePurpose
BOSdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling