3DZJ

Crystal structure of human CD38 extracellular domain E226Q mutant, 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
2.346.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.858α = 106.11
b = 53.228β = 91.97
c = 65.67γ = 95.03
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102006-02-21MSINGLE 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
11.93097.50.090.0921.23.8416333
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)
1.91.9895.20.4360.4362.92.9

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 1YH31.920389593895920611000.1880.1850.241RANDOM33.29
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]
-1.060.560.450.650.981.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.316
r_dihedral_angle_4_deg17.826
r_dihedral_angle_3_deg15.779
r_dihedral_angle_1_deg6.39
r_scangle_it4.537
r_scbond_it2.975
r_mcangle_it1.889
r_angle_refined_deg1.772
r_mcbond_it1.21
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.316
r_dihedral_angle_4_deg17.826
r_dihedral_angle_3_deg15.779
r_dihedral_angle_1_deg6.39
r_scangle_it4.537
r_scbond_it2.975
r_mcangle_it1.889
r_angle_refined_deg1.772
r_mcbond_it1.21
r_nbtor_refined0.314
r_nbd_refined0.228
r_xyhbond_nbd_refined0.163
r_symmetry_vdw_refined0.152
r_chiral_restr0.129
r_symmetry_hbond_refined0.109
r_bond_refined_d0.019
r_gen_planes_refined0.008
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 Atoms4010
Nucleic Acid Atoms
Solvent Atoms370
Heterogen Atoms44

Software

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