1VCR | pdb_00001vcr

An icosahedral assembly of light-harvesting chlorophyll a/b protein complex from pea thylakoid membranes

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Personal communication with Prof. W. Kuhlbrandt. Nature 367, 614-621, (1994)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	288	Potassium chloride, PEG4000, Xylitol, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 360.646	α = 90
b = 360.646	β = 90
c = 360.646	γ = 90

Symmetry
Space Group	F 2 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARRESEARCH		2000-05-22	M	SINGLE WAVELENGTH
2	1
3	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.000	SPring-8	BL41XU
2	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.000	SPring-8	BL38B1
3	SYNCHROTRON	SPRING-8 BEAMLINE BL40B2	1.000	SPring-8	BL40B2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	9.5	500	99.9	0.085	3	8	2534	2532			296

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)
	9.5	10.1	99.9		0.499	0.499	1.5	8.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Personal communication with Prof. W. Kuhlbrandt. Nature 367, 614-621, (1994)	9.5	20	2241	1935	188	86.3	0.379	0.43	0.353	0.44	RANDOM	296

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	496
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	300

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
CNS	refinement
CCP4	data scaling
CNS	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.