2FHJ | pdb_00002fhj

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
2.3748.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85α = 90
b = 74.15β = 113.54
c = 103.87γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDADSC 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)R Sym 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
1210494.70.1260.1057.9337716475995-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
22.191.70.5020.4133.382.859923

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ID 1FTR2207599575995387096.40.2210.2210.2190.230.2560.22RANDOM29.712
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]
4.911.84-2.9-0.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.876
r_dihedral_angle_4_deg17.427
r_dihedral_angle_3_deg15.148
r_dihedral_angle_1_deg8.311
r_scangle_it5.223
r_scbond_it3.454
r_mcangle_it1.856
r_angle_other_deg1.77
r_angle_refined_deg1.613
r_mcbond_it1.136
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.876
r_dihedral_angle_4_deg17.427
r_dihedral_angle_3_deg15.148
r_dihedral_angle_1_deg8.311
r_scangle_it5.223
r_scbond_it3.454
r_mcangle_it1.856
r_angle_other_deg1.77
r_angle_refined_deg1.613
r_mcbond_it1.136
r_mcbond_other0.371
r_nbd_refined0.254
r_symmetry_vdw_refined0.243
r_symmetry_vdw_other0.24
r_xyhbond_nbd_refined0.206
r_symmetry_hbond_refined0.201
r_nbd_other0.193
r_nbtor_refined0.191
r_metal_ion_refined0.181
r_nbtor_other0.091
r_chiral_restr0.072
r_xyhbond_nbd_other0.022
r_bond_refined_d0.011
r_bond_other_d0.006
r_gen_planes_refined0.006
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8950
Nucleic Acid Atoms
Solvent Atoms451
Heterogen Atoms417

Software

Software
Software NamePurpose
DENZOdata reduction
XSCALEdata scaling
EPMRphasing
REFMACrefinement