5VYQ

Crystal structure of the N-formyltransferase Rv3404c from mycobacterium tuberculosis in complex with YDP-Qui4N and folinic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4PZU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829320% PEG-8000, 100 mM HEPPS, 200 mM KCl, 5 mM TDP-Qui4N, 5 mM folinic acid
Crystal Properties
Matthews coefficientSolvent content
2.5952.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.486α = 90
b = 73.018β = 90
c = 173.265γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135montel2017-01-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
11.65099.10.07812.46.479772
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)
11.61.796.80.3512.53.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4pzu1.65075782399099.10.168410.166730.20025RANDOM17.699
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]
0.67-0.03-0.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.211
r_dihedral_angle_4_deg16.192
r_dihedral_angle_3_deg11.655
r_long_range_B_refined6.567
r_long_range_B_other6.567
r_dihedral_angle_1_deg6.088
r_scangle_other4.539
r_scbond_it2.964
r_scbond_other2.955
r_mcangle_other2.575
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.211
r_dihedral_angle_4_deg16.192
r_dihedral_angle_3_deg11.655
r_long_range_B_refined6.567
r_long_range_B_other6.567
r_dihedral_angle_1_deg6.088
r_scangle_other4.539
r_scbond_it2.964
r_scbond_other2.955
r_mcangle_other2.575
r_mcangle_it2.574
r_angle_refined_deg1.913
r_mcbond_it1.761
r_mcbond_other1.756
r_angle_other_deg0.938
r_chiral_restr0.112
r_bond_refined_d0.011
r_gen_planes_refined0.008
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3741
Nucleic Acid Atoms
Solvent Atoms666
Heterogen Atoms151

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing