4QHV

Crystal structure of human dihydrofolate reductase as complex with pyridopyrimidine 22 (N~6~-METHYL-N~6~-[4-(PROPAN-2-YL)PHENYL]PYRIDO[2,3-D]PYRIMIDINE-2,4,6-TRIAMINE)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1U72 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP628760% AmSO4,3% v/v ETOH, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Crystal Properties
Matthews coefficientSolvent content
2.5151.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.393α = 90
b = 84.393β = 90
c = 78.333γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113PIXELDECTRIS PILATUS 6Mmirrors2013-06-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.975SSRLBL11-1

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
11.5434.592.80.0260.0221.32.572513287622229.6
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)
11.541.6275.40.1790.234.52.33398

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)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 REPLACEMENTTHROUGHOUT1u721.6134.52222727524506128995.680.1890.179190.177050.22129RANDOM19.076
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.054
r_dihedral_angle_3_deg15.215
r_dihedral_angle_4_deg10.18
r_dihedral_angle_1_deg6.572
r_angle_refined_deg2.86
r_chiral_restr0.209
r_bond_refined_d0.025
r_gen_planes_refined0.015
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1502
Nucleic Acid Atoms
Solvent Atoms154
Heterogen Atoms101

Software

Software
Software NamePurpose
XDSdata scaling
MOLREPphasing
REFMACrefinement
XDSdata reduction
SCALEPACKdata scaling