2FHK

Crystal structure of formylmethanofuran: tetrahydromethanopterin formyltransferase in complex with its coenzymes


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FTRPDB ID 1FTR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729812-18 % PEG 8000, 20 % glycerol, 0.5 M KCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3948.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86α = 90
b = 74.2β = 113.6
c = 103.6γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray281CCDADSC QUANTUM 42004-04-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.91ESRFID14-4

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
1210498.10.1567.6480885
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)
22.196.60.4433.9110589

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 ID 1FTR2208058780587403099.750.2190.2190.2180.245RANDOM19.398
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]
2.641.07-0.8-0.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.6
r_dihedral_angle_3_deg13.171
r_dihedral_angle_4_deg11.879
r_scangle_it6.502
r_dihedral_angle_1_deg5.347
r_scbond_it4.016
r_mcangle_it2.175
r_angle_refined_deg1.152
r_mcbond_it1.087
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.6
r_dihedral_angle_3_deg13.171
r_dihedral_angle_4_deg11.879
r_scangle_it6.502
r_dihedral_angle_1_deg5.347
r_scbond_it4.016
r_mcangle_it2.175
r_angle_refined_deg1.152
r_mcbond_it1.087
r_nbtor_refined0.301
r_symmetry_vdw_refined0.284
r_symmetry_hbond_refined0.226
r_nbd_refined0.216
r_xyhbond_nbd_refined0.139
r_metal_ion_refined0.112
r_symmetry_metal_ion_refined0.081
r_chiral_restr0.069
r_bond_refined_d0.009
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8897
Nucleic Acid Atoms
Solvent Atoms474
Heterogen Atoms113

Software

Software
Software NamePurpose
DENZOdata reduction
XSCALEdata scaling
EPMRphasing
REFMACrefinement