2I37 | pdb_00002i37

Crystal structure of a photoactivated rhodopsin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2I36	PDB entry 2I36

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.3	278	80 mM MES, pH 6.3, 110 mM N-nonyl-beta-D-glucoside, 200 mM zinc acetate, 0.1% sodium azide, 16 mM beta-mercaptoethanol, 2.6% Merpol HCS, equilibrated against 3.1-3.3 M ammonium sulfate, VAPOR DIFFUSION, temperature 278K

Crystal Properties
Matthews coefficient	Solvent content
4.59	73.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 161.245	α = 90
b = 161.245	β = 90
c = 143.442	γ = 120

Symmetry
Space Group	P 31 1 2

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		2005-11-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.97620	SLS	X06SA

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	4.15	50	76.8	0.063	11.1	8.9	12498	12498

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	4.15	4.3	61.2		0.86		3.3	981

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 2I36	4.15	30	12455	12455	645	76.78	0.378	0.378	0.377	0.38	0.382	0.38	RANDOM	177.21

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]
-14.29	-7.14		-14.29		21.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.147
r_dihedral_angle_4_deg	20.403
r_dihedral_angle_3_deg	18.005
r_dihedral_angle_1_deg	6.048
r_angle_refined_deg	1.069
r_angle_other_deg	0.772
r_symmetry_hbond_refined	0.336
r_symmetry_vdw_refined	0.245
r_symmetry_vdw_other	0.204
r_nbd_refined	0.184
r_nbtor_refined	0.184
r_nbd_other	0.169
r_xyhbond_nbd_refined	0.142
r_nbtor_other	0.084
r_chiral_restr	0.058
r_bond_refined_d	0.007
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7577
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	237

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing