Experiment: 7C52

Co-crystal structure of a photosynthetic LH1-RC in complex with electron donor HiPIP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5Y5S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	5	293	PEG 1500, sodium succinate, calcium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.97	52.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.435	α = 90
b = 183.335	β = 112.584
c = 123.857	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2017-02-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	0.98	Photon Factory	BL-17A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	2.89	48.2	97.4	0.127	0.998	10.3	6.5		86259			103.66

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.893	2.996	87.7		2.06	0.334	0.69

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5Y5S	2.89	29.99	1.33	86259	4311	97.57	0.2203	0.2188	0.2258	0.2477	0.256	128.67

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	21.054
f_angle_d	1.2322
f_chiral_restr	0.0598
f_plane_restr	0.0081
f_bond_d	0.0055

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	26183
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	1165

Software

Software
Software Name	Purpose
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building
PHENIX	refinement