1FBK | pdb_00001fbk

CRYSTAL STRUCTURE OF CYTOPLASMICALLY OPEN CONFORMATION OF BACTERIORHODOPSIN

ELECTRON CRYSTALLOGRAPHY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	naturally occurring in vivo	7	310	crystals are increased in size by fusion and annealing using detergents, pH 7, naturally occurring in vivo, temperature 37K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.45	α = 90
b = 62.45	β = 90
c = 100.9	γ = 120

Symmetry
Space Group	P 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	electron	93	CCD	OTHER		1998-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ELECTRON MICROSCOPE	OTHER

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	3.2	200	77.7	0.173			7298	5668

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
ELECTRON CRYSTALLOGRAPHY		3.2	200	7298	5668	610	77.7	0.272	0.321	RANDOM

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
c_angle_deg	1.4
c_bond_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1726
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	20

Software

Software
Software Name	Purpose
CNS	refinement

Sample
CYTOPLASMICALLY OPEN CONFORMATION OF BACTERIORHODOPSIN

Specimen Preparation
Sample Aggregation State	2D ARRAY
Embedding Material	glucose or trehalose
Embedding Details

3D Reconstruction
Reconstruction Method	CRYSTALLOGRAPHY
Number of Particles
Reported Resolution (Å)	3.2
Resolution Method	DIFFRACTION PATTERN/LAYERLINES
Other Details	402 patterns merged (merging R 17.3%) to generate set of lattice lines covering ~87% of reciprocal space, with resolution of 3.2 A in-plane and 3.6 A ...	402 patterns merged (merging R 17.3%) to generate set of lattice lines covering ~87% of reciprocal space, with resolution of 3.2 A in-plane and 3.6 A vertically [primary citation]
Refinement Type
Symmetry Type
Space Group Name	P 3
Length a	62.45
Length b	62.45
Angle Gamma	120

Data Acquisition
Detector Type	GENERIC CCD
Electron Dose (electrons/Å**2)

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI/PHILIPS CM12
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	DIFFRACTION
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source
Acceleration Voltage (kV)
Imaging Details	imaging date 1998-12-01

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.