2CFI | pdb_00002cfi

The hydrolase domain of human 10-FTHFD in complex with 6- formyltetrahydropterin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BW0PDB ENTRY 2BW0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.81.4 M AMMONIUM SULFATE, 50 MM HEPES PH 7.8
Crystal Properties
Matthews coefficientSolvent content
2.6152.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.14α = 90
b = 64.44β = 98.79
c = 58.87γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.1BESSY14.1

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
11.852099.60.0714.34.834108-3
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)
11.851.999.50.4144.5

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2BW01.851032226169699.70.1810.1780.190.2250.24RANDOM31.77
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]
1.13-0.3-0.83-0.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.59
r_dihedral_angle_4_deg17.005
r_dihedral_angle_3_deg14.7
r_dihedral_angle_1_deg6.766
r_scangle_it3.501
r_scbond_it2.54
r_mcangle_it2.104
r_angle_refined_deg1.575
r_mcbond_it1.349
r_angle_other_deg1.068
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.59
r_dihedral_angle_4_deg17.005
r_dihedral_angle_3_deg14.7
r_dihedral_angle_1_deg6.766
r_scangle_it3.501
r_scbond_it2.54
r_mcangle_it2.104
r_angle_refined_deg1.575
r_mcbond_it1.349
r_angle_other_deg1.068
r_symmetry_vdw_other0.218
r_nbd_refined0.211
r_nbd_other0.201
r_xyhbond_nbd_refined0.196
r_nbtor_refined0.181
r_symmetry_hbond_refined0.181
r_chiral_restr0.16
r_symmetry_vdw_refined0.109
r_nbtor_other0.087
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2409
Nucleic Acid Atoms
Solvent Atoms303
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling