4X32 | pdb_00004x32

Bacteriorhodopsin ground state structure collected in cryo conditions from crystals obtained in LCP with PEG as a precipitant.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NTU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE	5.6	294	27% PEG2000, 100 mM phosphate buffer pH 5.6

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.525	α = 90
b = 60.525	β = 90
c = 101.48	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	100	PIXEL	PSI PILATUS 6M		2014-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	1.9	46.57	100	0.095	0.026	1	17.9	14.1	16647	16643			33.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.94	100		1.867	0.496	0.548	1.8	14.3	1072

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2NTU	1.9	52.42	15773	841	99.98	0.1737	0.1715	0.18	0.2143	0.22	RANDOM	36.741

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]
-1.03	-0.51		-1.03		3.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.888
r_dihedral_angle_3_deg	12.706
r_dihedral_angle_4_deg	11.915
r_dihedral_angle_1_deg	4.646
r_mcangle_it	1.92
r_mcbond_other	1.349
r_mcbond_it	1.348
r_angle_refined_deg	1.223
r_angle_other_deg	0.768
r_chiral_restr	0.072

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.888
r_dihedral_angle_3_deg	12.706
r_dihedral_angle_4_deg	11.915
r_dihedral_angle_1_deg	4.646
r_mcangle_it	1.92
r_mcbond_other	1.349
r_mcbond_it	1.348
r_angle_refined_deg	1.223
r_angle_other_deg	0.768
r_chiral_restr	0.072
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1710
Nucleic Acid Atoms
Solvent Atoms	30
Heterogen Atoms	124

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
PHASER	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.