1ALY

CRYSTAL STRUCTURE OF HUMAN CD40 LIGAND


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelModelArchivema-cem76ENTRY 1CDA that was moved from PDB to ModelArchive

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5PROTEIN WAS CRYSTALLIZED FROM 1.4 M NA CITRATE, 50 MM HEPES PH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.9762.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.17α = 90
b = 77.17β = 90
c = 90.46γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray123AREA DETECTORSIEMENSMIRRORS1994-01-11M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1

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
11.7510077.10.0670.0566.52.71425872
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)
1.751.8446.10.0560.153.91.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 1CDA27.5210990109982.30.2230.2230.295RANDOM
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]
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1374
Nucleic Acid Atoms
Solvent Atoms192
Heterogen Atoms

Software

Software
Software NamePurpose
XDSdata scaling
BUDDHAdata reduction
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
BUDDHAdata scaling
X-PLORphasing