4QRY | pdb_00004qry

the ground state and the N intermediate of pharaonis halorhodopsin in complex with bromide ion

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	278	The C2 crystal of halorhodopsin grew when a solution containing 3 mg/ml halorhodopsin, 0.4 % nonylglucoside, 1 M ammonium sulfate, 0.16 M sodium chloride, 0.04 M sodium citrate at pH 6 and 0.04 % sodium azide was concentrated by the vapor diffusion using a reservoir solution containing 2.8 M ammonium sulfate and 0.12 M sodium citrate at pH 6. For investigation of light-induced structural changes, the C2 crystal was soaked in a solution containing 0.1 M sodium bromide, 1.5 M trisodium citrate at pH 7 and 30 % trehalose. This crystal was illuminated at 240 K with orange light and cooled to 100 K at a rate of 2.3 K/sec in the dark., VAPOR DIFFUSION, SITTING DROP, temperature 278K

Crystal Properties
Matthews coefficient	Solvent content
1.6	23.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 153.36	α = 90
b = 98.3	β = 128.13
c = 100.53	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		2014-06-03	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	2.2	49.13	99	0.1	0.1	9.2	3.2	59552	58957	2.5	2.5	22.8

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	2.2	2.32	98.5		0.5	0.5	2.7	3.3	8518

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3qbk	2.2	15	59422	58744	2967	98.9	0.214	0.214	0.21	0.2428	0.24	RANDOM	24.9699

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]
0.976		2.474	3.066		-4.042

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	18.9
c_angle_d	1.22
c_improper_angle_d	0.8
c_bond_d	0.0067

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11759
Nucleic Acid Atoms
Solvent Atoms	288
Heterogen Atoms	357

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.