6ECQ

The human methylenetetrahydrofolate dehydrogenase/cyclohydrolase (FolD) complexed with NADP and inhibitor LY345899


X-RAY DIFFRACTION

Starting Model(s)

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

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 = 67.49α = 90
b = 136.37β = 90
c = 61.38γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IICMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
12.72097.10.1351568815688-3-3
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)
12.72.7495.90.3325

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 SYNTHESISTHROUGHOUT1DIB2.719.613706154894.370.185920.179050.24725RANDOM24.615
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]
-0.220.55-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.224
r_dihedral_angle_4_deg16.927
r_dihedral_angle_3_deg15.587
r_dihedral_angle_1_deg5.975
r_long_range_B_refined4.393
r_long_range_B_other4.377
r_scangle_other2.614
r_mcangle_other2.181
r_mcangle_it2.18
r_angle_refined_deg1.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.224
r_dihedral_angle_4_deg16.927
r_dihedral_angle_3_deg15.587
r_dihedral_angle_1_deg5.975
r_long_range_B_refined4.393
r_long_range_B_other4.377
r_scangle_other2.614
r_mcangle_other2.181
r_mcangle_it2.18
r_angle_refined_deg1.55
r_scbond_other1.532
r_scbond_it1.531
r_mcbond_it1.292
r_mcbond_other1.29
r_angle_other_deg0.963
r_chiral_restr0.082
r_bond_refined_d0.011
r_gen_planes_refined0.006
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 Atoms4412
Nucleic Acid Atoms
Solvent Atoms100
Heterogen Atoms130

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing