Experiment: 5B6W

A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 16 ns after photoexcitation

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5B6V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE		293	0.1M Na/K phosphate pH5.4, 30% PEG 2000

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.5	α = 90
b = 62.5	β = 90
c = 112	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	CCD	MPCCD		2016-02-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SACLA BEAMLINE BL3	1.63	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	2.1	39.92	100	7.7	177		14513

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	2.07

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	5B6V	2.1	21.912	1.4	14473	719	99.98	0.157	0.1559	0.1604	0.1747	0.1786

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	17.316
f_angle_d	0.86
f_chiral_restr	0.038
f_plane_restr	0.004
f_bond_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1787
Nucleic Acid Atoms
Solvent Atoms	17
Heterogen Atoms	242

Software

Software
Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling