5B35

Serial Femtosecond Crystallography (SFX) of Ground State Bacteriorhodopsin Crystallized from Bicelles Determined Using 7-keV X-ray Free Electron Laser (XFEL) at SACLA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5B34	PDB ID: 5B34

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		293	25%(w/v) DMPC/CHAPSO bicelles, 3.2 M NaH2PO4, 3.5%(w/v) triethylene glycol, 180 mM 1,6-hexanediol

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.2	α = 90
b = 103	β = 90
c = 128.7	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	CCD	MPCCD		2014-02-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SACLA BEAMLINE BL3	1.771	SACLA	BL3

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	2.35	50	100	4.83	80.9		13212

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	2.35	2.42

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	PDB ID: 5B34	2.35	50	12535	650	99.97	0.16905	0.16633	0.21978	RANDOM	66.323

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]
0.18			0.14		-0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.806
r_dihedral_angle_3_deg	17.703
r_dihedral_angle_4_deg	16.393
r_long_range_B_refined	9.102
r_long_range_B_other	9.097
r_scangle_other	7.643
r_dihedral_angle_1_deg	5.401
r_scbond_it	5.342
r_scbond_other	5.34
r_mcangle_other	5.046
r_mcangle_it	5.044
r_mcbond_it	3.832
r_mcbond_other	3.82
r_angle_refined_deg	1.945
r_angle_other_deg	1.087
r_chiral_restr	0.102
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1745
Nucleic Acid Atoms
Solvent Atoms	36
Heterogen Atoms	205

Software

Software
Software Name	Purpose
REFMAC	refinement
Cheetah	data extraction
CrystFEL	data processing
SHELX	phasing