3DCJ

Crystal structure of glycinamide formyltransferase (PurN) from Mycobacterium tuberculosis in complex with 5-methyl-5,6,7,8-tetrahydrofolic acid derivative


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MEOPDB entry 1MEO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529120% PEG 3350, 0.2 M Mg nitrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.5651.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.153α = 90
b = 61.66β = 103.31
c = 61.525γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2007-03-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.54178

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.232.58100224712247121.59
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.22.34100

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 1MEO2.232.582247122471113897.030.18680.183790.24286RANDOM19.894
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]
-0.03-0.040.03-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.821
r_dihedral_angle_4_deg20.327
r_dihedral_angle_3_deg15.47
r_dihedral_angle_1_deg6.405
r_scangle_it4.712
r_scbond_it2.955
r_angle_refined_deg1.859
r_mcangle_it1.639
r_mcbond_it0.934
r_chiral_restr0.118
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.821
r_dihedral_angle_4_deg20.327
r_dihedral_angle_3_deg15.47
r_dihedral_angle_1_deg6.405
r_scangle_it4.712
r_scbond_it2.955
r_angle_refined_deg1.859
r_mcangle_it1.639
r_mcbond_it0.934
r_chiral_restr0.118
r_bond_refined_d0.022
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3014
Nucleic Acid Atoms
Solvent Atoms286
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement