3DZK

Crystal structure of human CD38 extracellular domain, NMN 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
2.346.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.889α = 106.2
b = 53.205β = 91.84
c = 65.598γ = 95.05
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102006-05-01MSINGLE 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
11.83096.70.0990.09912.63.4472291.5
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)
1.81.8687.20.4430.4431.52

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 1YH31.8120447394473923831000.1760.1740.217RANDOM33.12
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]
-0.710.160.150.320.60.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.719
r_dihedral_angle_4_deg22.069
r_dihedral_angle_3_deg15.886
r_dihedral_angle_1_deg5.871
r_scangle_it4.051
r_scbond_it2.615
r_mcangle_it1.56
r_angle_refined_deg1.523
r_mcbond_it0.98
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.719
r_dihedral_angle_4_deg22.069
r_dihedral_angle_3_deg15.886
r_dihedral_angle_1_deg5.871
r_scangle_it4.051
r_scbond_it2.615
r_mcangle_it1.56
r_angle_refined_deg1.523
r_mcbond_it0.98
r_nbtor_refined0.312
r_nbd_refined0.228
r_symmetry_vdw_refined0.203
r_xyhbond_nbd_refined0.162
r_symmetry_hbond_refined0.124
r_chiral_restr0.109
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 Atoms
Solvent Atoms354
Heterogen Atoms44

Software

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