5J7A

Bacteriorhodopsin ground state structure obtained with Serial Femtosecond Crystallography

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1H68

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE	5.6	293	Precipitant: 29%-38% PEG 2000, 100 mM phosphate buffer pH 5.6. MAG 9.9 used for LCP formation. Crystallization setup in Hamilton syringe with tube of LCP surrounded by precipitant.

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62	α = 90
b = 62	β = 90
c = 110	γ = 120

Symmetry
Space Group	P 63

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	PIXEL	CS-PAD CXI-2		2014-06-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SLAC LCLS BEAMLINE CXI	1.83	SLAC LCLS	CXI

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.3	21.9	99.98	6.56	163		11027			31.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.41	99.86		1.58	16.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1H68	2.3	21.66	10010	650	99.87	0.1926	0.191	0.2181	RANDOM	39.282

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]
1.45	0.72		1.45		-4.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.63
r_dihedral_angle_4_deg	16.008
r_dihedral_angle_3_deg	13.32
r_dihedral_angle_1_deg	4.452
r_angle_refined_deg	1.165
r_angle_other_deg	0.89
r_mcangle_it	0.694
r_mcbond_it	0.37
r_mcbond_other	0.37
r_chiral_restr	0.059

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.63
r_dihedral_angle_4_deg	16.008
r_dihedral_angle_3_deg	13.32
r_dihedral_angle_1_deg	4.452
r_angle_refined_deg	1.165
r_angle_other_deg	0.89
r_mcangle_it	0.694
r_mcbond_it	0.37
r_mcbond_other	0.37
r_chiral_restr	0.059
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1715
Nucleic Acid Atoms
Solvent Atoms	17
Heterogen Atoms	77

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	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.