6ECP

The human methylenetetrahydrofolate dehydrogenase/cyclohydrolase (FolD) complexed with NADP and inhibitor LY249543


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DIA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.2293PEG 3350, GLYCEROL, SODIUM CITRATE, AMMONIUM ACETATE, pH 5.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 20K
Crystal Properties
Matthews coefficientSolvent content
2.244.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.871α = 90
b = 136.396β = 90
c = 61.649γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 41999-03-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X8C1.0NSLSX8C

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
12.21599.30.0445429674-325
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)
12.22.2395.50.1464

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1DIA2.214.8626078288497.210.178840.173490.22671RANDOM25.614
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]
-0.090.48-0.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.815
r_dihedral_angle_4_deg15.668
r_dihedral_angle_3_deg14.212
r_long_range_B_refined6.467
r_long_range_B_other6.459
r_dihedral_angle_1_deg6.069
r_scangle_other4.321
r_mcangle_it2.935
r_mcangle_other2.935
r_scbond_other2.771
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.815
r_dihedral_angle_4_deg15.668
r_dihedral_angle_3_deg14.212
r_long_range_B_refined6.467
r_long_range_B_other6.459
r_dihedral_angle_1_deg6.069
r_scangle_other4.321
r_mcangle_it2.935
r_mcangle_other2.935
r_scbond_other2.771
r_scbond_it2.77
r_mcbond_it1.971
r_mcbond_other1.969
r_angle_refined_deg1.728
r_angle_other_deg1.017
r_chiral_restr0.106
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms4412
Nucleic Acid Atoms
Solvent Atoms195
Heterogen Atoms160

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing