3DZI

Crystal structure of human CD38 extracellular domain, ribose-5'-phosphate intermediate/GTP complex


X-RAY DIFFRACTION

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
2.2344.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.669α = 106.09
b = 52.747β = 91.92
c = 65.133γ = 95.27
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102006-05-06MSINGLE 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
11.733095.50.0420.04225.83.6535192
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)
1.731.7982.20.4580.45822.8

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 1YH31.73205023850238269195.80.1790.1770.211RANDOM40.48
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]
-1.230.420.440.661.171.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.723
r_dihedral_angle_4_deg17.108
r_dihedral_angle_3_deg16.06
r_dihedral_angle_1_deg6.012
r_scangle_it4.046
r_scbond_it2.535
r_angle_refined_deg1.566
r_mcangle_it1.53
r_mcbond_it0.959
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.723
r_dihedral_angle_4_deg17.108
r_dihedral_angle_3_deg16.06
r_dihedral_angle_1_deg6.012
r_scangle_it4.046
r_scbond_it2.535
r_angle_refined_deg1.566
r_mcangle_it1.53
r_mcbond_it0.959
r_nbtor_refined0.314
r_nbd_refined0.232
r_symmetry_vdw_refined0.223
r_symmetry_hbond_refined0.157
r_xyhbond_nbd_refined0.154
r_chiral_restr0.105
r_bond_refined_d0.016
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 Atoms45
Solvent Atoms344
Heterogen Atoms45

Software

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