3C9M | pdb_00003c9m

Structure of a mutant bovine rhodopsin in hexagonal crystal form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2J4Y	The A chain of PDB entry 2J4Y, after suitable transformation into this space group.

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
3.43	64.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.3	α = 90
b = 109.3	β = 90
c = 77.7	γ = 120

Symmetry
Space Group	P 64

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray						M	SINGLE WAVELENGTH

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION		The A chain of PDB entry 2J4Y, after suitable transformation into this space group.	3.4	40.42	2.05	7353	341	99.8	0.176	0.174	0.17	0.219	0.2	72.082

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]
0.981			0.981		-1.961

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	20.334
f_angle_d	1.495
f_chiral_restr	0.142
f_bond_d	0.012
f_plane_restr	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2589
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	37

Software

Software
Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
REFMAC	refinement