4XJS

Human CD38 complexed with inhibitor 1 [6-fluoro-2-methyl-4-[(2,3,6-trichlorobenzyl)amino]quinoline-8-carboxamide]


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YH3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5295Protein concentration was 7mgs/ml. Crystals were grown from 23% PEG3350, 0.1mM BisTrisPropane at 22 deg C (2+2uL drops over a 500uL well). Crystals were soaked with 5mM inhibitor for 24 hours prior to data collection. Crystals were flash frozen in PFO.
Crystal Properties
Matthews coefficientSolvent content
1.9536.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.298α = 90
b = 64.424β = 90
c = 72.832γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDRIGAKU SATURN 944+2011-01-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.54

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
12.834.8980.09296.65790
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)
12.82.8799.50.594.87

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 REPLACEMENTTHROUGHOUT1YH32.834.8579029398.450.18990.18630.2634RANDOM53.927
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]
0.01-0.120.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.038
r_dihedral_angle_4_deg15.953
r_dihedral_angle_3_deg14.175
r_dihedral_angle_1_deg5.427
r_mcangle_it1.961
r_angle_refined_deg1.239
r_mcbond_it1.202
r_mcbond_other1.191
r_angle_other_deg0.792
r_chiral_restr0.065
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.038
r_dihedral_angle_4_deg15.953
r_dihedral_angle_3_deg14.175
r_dihedral_angle_1_deg5.427
r_mcangle_it1.961
r_angle_refined_deg1.239
r_mcbond_it1.202
r_mcbond_other1.191
r_angle_other_deg0.792
r_chiral_restr0.065
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1886
Nucleic Acid Atoms
Solvent Atoms23
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling
REFMACphasing