1RWT | pdb_00001rwt

Crystal Structure of Spinach Major Light-harvesting complex at 2.72 Angstrom Resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	291	Citrate trisodium, beta-nonyl-glucoside, deoxy-bigchap, DGDG, Hepes, pH 7.5, VAPOR DIFFUSION, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
5.36	76.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 261.787	α = 90
b = 261.787	β = 90
c = 660.498	γ = 120

Symmetry
Space Group	H 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV		2002-11-20	M	SINGLE WAVELENGTH
2	1	100	IMAGE PLATE	MARRESEARCH		2003-06-12

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-6B	1.0	Photon Factory	BL-6B
2	SYNCHROTRON	BSRF BEAMLINE 3W1A	1.0	BSRF	3W1A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.7	25	90.8	0.082	14.4	5.2	211079	191660		-3	20.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.75	79.6		0.368	2.5		9188

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SIR in combination with real-space averaging refinement and extension	THROUGHOUT	2.72	10	197822	188496	9326	83	0.207	0.194	0.194	0.18	0.221	0.2	RANDOM	31.3

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]
0.02	5.23		0.02		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	25.7
c_improper_angle_d	2.66
c_angle_deg	2.3
c_bond_d	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16619
Nucleic Acid Atoms
Solvent Atoms	699
Heterogen Atoms	11721

Software

Software
Software Name	Purpose
CNS	refinement
MAR345	data collection
SCALEPACK	data scaling
MLPHARE	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.