4X31

Room temperature structure of bacteriorhodopsin from lipidic cubic phase obtained with serial millisecond crystallography using synchrotron radiation

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	294	Precipitant: 27%-39% 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
2.49	50.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.79	α = 90
b = 62.79	β = 90
c = 109.67	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	294	CCD	RAYONIX MX-225		2014-05-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID13	1.0	ESRF	ID13

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	2.4	36.56	100	0.224	3.57	127	9655	9655

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	2.4	2.46	100		1.16	88.8

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	THROUGHOUT	1H68	2.4	31.4	9633	441	99.96	0.2072	0.2053	0.249	RANDOM	58.52

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]
2.28	1.14		2.28		-7.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.914
r_dihedral_angle_4_deg	15.673
r_dihedral_angle_3_deg	14.77
r_dihedral_angle_1_deg	4.54
r_mcangle_it	2.673
r_mcbond_it	1.485
r_mcbond_other	1.483
r_angle_refined_deg	1.013
r_angle_other_deg	0.749
r_chiral_restr	0.052

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.914
r_dihedral_angle_4_deg	15.673
r_dihedral_angle_3_deg	14.77
r_dihedral_angle_1_deg	4.54
r_mcangle_it	2.673
r_mcbond_it	1.485
r_mcbond_other	1.483
r_angle_refined_deg	1.013
r_angle_other_deg	0.749
r_chiral_restr	0.052
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	1756
Nucleic Acid Atoms
Solvent Atoms	10
Heterogen Atoms	82

Software

Software
Software Name	Purpose
REFMAC	refinement
PHASER	phasing
PDB_EXTRACT	data extraction

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.