Experiment: 3QBI

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3A7K	PDB ENTRY 3A7K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	288	Crystallization: 3.5 mg/ml halorhodopsin, 5mg/ml nonylglucoside, 2.8M ammonium sulfate, 0.1 M glycine, 0.1M NaCl Post-crystallization soaking: 3 M ammonium sulfate, 0.2 M glycine (pH10.0), 30% trehalose , pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 288K

Crystal Properties
Matthews coefficient	Solvent content
3.19	61.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 153.96	α = 90
b = 97.97	β = 128.68
c = 100.65	γ = 90

Symmetry
Space Group	C 1 2 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	CCD	ADSC QUANTUM 315	mirrors	2010-10-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.0	SPring-8	BL38B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.1	48.9	99.2	0.102	0.102	9.5	3.2	67957	67414			23.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.21	99.2		0.54	0.54	1.4	3.2	9782

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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 ENTRY 3A7K	2.1	15	67894	67243	3429	99	0.235	0.235	0.266	RANDOM	29.183

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]
1.653		-0.322	4.528		-6.181

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	18.41146
c_scangle_it	2.42
c_mcangle_it	1.83
c_scbond_it	1.816
c_mcbond_it	1.228
c_angle_d	1.10697
c_improper_angle_d	0.78623
c_bond_d	0.006297

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5897
Nucleic Acid Atoms
Solvent Atoms	212
Heterogen Atoms	198

Software

Software
Software Name	Purpose
ADSC	data collection
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
CNS	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.