3DZG

Crystal structure of human CD38 extracellular domain, ara-F-ribose-5'-phosphate/nicotinamide complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YH3PDB ENTRY 1YH3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16298100 mM MES pH 6.0, 15% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.2645.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.689α = 106.06
b = 52.812β = 91.95
c = 65.381γ = 95.12
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102007-04-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE A1CHESSA1

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
11.643096.30.0560.05617.53.5619885
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)
11.641.786.90.1890.1895.73

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1YH31.6520588335883331381000.1760.1740.211RANDOM32.24
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]
-0.730.510.490.340.941.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.806
r_dihedral_angle_4_deg17.6
r_dihedral_angle_3_deg15.211
r_dihedral_angle_1_deg5.853
r_scangle_it3.777
r_scbond_it2.415
r_angle_refined_deg1.504
r_mcangle_it1.483
r_mcbond_it0.901
r_nbtor_refined0.316
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.806
r_dihedral_angle_4_deg17.6
r_dihedral_angle_3_deg15.211
r_dihedral_angle_1_deg5.853
r_scangle_it3.777
r_scbond_it2.415
r_angle_refined_deg1.504
r_mcangle_it1.483
r_mcbond_it0.901
r_nbtor_refined0.316
r_nbd_refined0.22
r_symmetry_vdw_refined0.207
r_symmetry_hbond_refined0.179
r_xyhbond_nbd_refined0.16
r_chiral_restr0.102
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4100
Nucleic Acid Atoms
Solvent Atoms468
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing