4XJT

Human CD38 complexed with inhibitor 2 [4-[(2,6-dimethylbenzyl)amino]-2-methylquinoline-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 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
1.9536.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.017α = 90
b = 63.95β = 90
c = 72.308γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDRIGAKU SATURN 944+2009-04-10MSINGLE 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
12.636.1990.09266.97323
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)
12.62.661000.474.77

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 REPLACEMENTTHROUGHOUT1YH32.636.1732335299.960.19420.19120.2538RANDOM48.013
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]
0.24-0.530.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.21
r_dihedral_angle_4_deg15.536
r_dihedral_angle_3_deg13.605
r_dihedral_angle_1_deg5.369
r_mcangle_it2.751
r_mcbond_it1.64
r_mcbond_other1.637
r_angle_refined_deg1.322
r_angle_other_deg0.761
r_chiral_restr0.066
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.21
r_dihedral_angle_4_deg15.536
r_dihedral_angle_3_deg13.605
r_dihedral_angle_1_deg5.369
r_mcangle_it2.751
r_mcbond_it1.64
r_mcbond_other1.637
r_angle_refined_deg1.322
r_angle_other_deg0.761
r_chiral_restr0.066
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1903
Nucleic Acid Atoms
Solvent Atoms47
Heterogen Atoms63

Software

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