6FMD

Targeting myeloid differentiation using potent human dihydroorotate dehydrogenase (hDHODH) inhibitors based on 2-hydroxypyrazolo[1,5-a]pyridine scaffold


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5MUT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.22930.2M KBr, 0.2M KSCN, 0.1M NaAc pH 5.2, 25% PEG 400, 2% PGA-LM
Crystal Properties
Matthews coefficientSolvent content
3.3763.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.441α = 90
b = 90.441β = 90
c = 122.446γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2017-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.97242ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.5878.32499.60.0710.080.036114.679465
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.581.6799.70.740.740.8350.3814.7

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5MUT1.5878.3275404401699.530.1380.13680.1597RANDOM26.408
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_deg36.175
r_sphericity_free30.319
r_dihedral_angle_4_deg17.739
r_sphericity_bonded14.134
r_dihedral_angle_3_deg11.341
r_dihedral_angle_1_deg5.446
r_rigid_bond_restr2.462
r_angle_refined_deg1.647
r_angle_other_deg1.016
r_chiral_restr0.096
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.175
r_sphericity_free30.319
r_dihedral_angle_4_deg17.739
r_sphericity_bonded14.134
r_dihedral_angle_3_deg11.341
r_dihedral_angle_1_deg5.446
r_rigid_bond_restr2.462
r_angle_refined_deg1.647
r_angle_other_deg1.016
r_chiral_restr0.096
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2731
Nucleic Acid Atoms
Solvent Atoms155
Heterogen Atoms181

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction