1ALY | pdb_00001aly

CRYSTAL STRUCTURE OF HUMAN CD40 LIGAND

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	ModelArchive	ma-cem76	ENTRY 1CDA that was moved from PDB to ModelArchive

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		PROTEIN WAS CRYSTALLIZED FROM 1.4 M NA CITRATE, 50 MM HEPES PH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.97	62.46

Crystal Data

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

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	123	AREA DETECTOR	SIEMENS	MIRRORS	1994-01-11	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.75	100	77.1	0.067	0.056	6.5	2.71		42587		2

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)	Redundancy	Number Unique Reflections (All)
	1.75	1.84	46.1		0.056	0.15	3.9	1.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1CDA	2	7.5	2	10990	1099	82.3	0.223	0.223	0.295	RANDOM

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 Atoms	Number
Protein Atoms	1374
Nucleic Acid Atoms
Solvent Atoms	192
Heterogen Atoms

Software

Software
Software Name	Purpose
XDS	data scaling
BUDDHA	data reduction
X-PLOR	model building
X-PLOR	refinement
XDS	data reduction
BUDDHA	data scaling
X-PLOR	phasing