2J4Y | pdb_00002j4y

Crystal structure of a rhodopsin stabilizing mutant expressed in mammalian cells

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GZM	PDB ENTRY 1GZM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5		VAPOUR DIFFUSION IN SITTING DROPS OF 10-15 MG/ML PROTEIN AND 0.2% C8E4,0.05%LDAO AGAINST 1.1-1.7M LITHIUM SULFATE, 0.1M HEPES PH 7.5

Crystal Properties
Matthews coefficient	Solvent content
3.64	58

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 31

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	MARRESEARCH	MICROFOCUSING	2004-06-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID13		ESRF	ID13

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	3.4	50	95.9	0.24	5.42	3.03		13689		-3	58.2

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	3.4	3.5	84.8		0.7	1.79	2.79

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	PDB ENTRY 1GZM	3.4	50	13689	407	95.9	0.2896	0.2896	0.26	0.3299	0.28	0.325	55.6579

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]
-3.497	-7.211		-3.497		6.994

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.40625
c_scangle_it	3.81
c_mcangle_it	3.13
c_scbond_it	2.39
c_mcbond_it	1.78
c_angle_deg	1.66
c_improper_angle_d	1.11414
c_bond_d	0.014
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5184
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	68

Software

Software
Software Name	Purpose
CNS	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing