Experiment: 4HYJ

Crystal structure of Exiguobacterium sibiricum rhodopsin

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DDL	Homology model based on PDB ENTRY 3DDL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Cubic phase crystallization		295	Cubic phase crystallization, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.099	α = 90
b = 96.099	β = 90
c = 124.38	γ = 120

Symmetry
Space Group	P 3 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	PIXEL	DECTRIS PILATUS 6M		2012-06-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.976	ESRF	ID23-1

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	2.15	69.17	98	0.054	12	3.9	36642	35982

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.42	96.7		0.334	3.7	3.8

Refinement

Statistics
Diffraction ID	Structure Solution 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	Homology model based on PDB ENTRY 3DDL	2.3	69.169	30116	29408	1498	97.65	0.1775	0.1754	0.1777	0.2149	0.2163	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
f_dihedral_angle_d	16.224
f_angle_d	1.401
f_chiral_restr	0.165
f_bond_d	0.008
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3494
Nucleic Acid Atoms
Solvent Atoms	33
Heterogen Atoms	343

Software

Software
Software Name	Purpose
MOLREP	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling