2I35

Crystal structure of rhombohedral crystal form of ground-state rhodopsin

X-RAY DIFFRACTION

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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, 16 mM beta-mercaptoethanol, 0.4% Merpol DA, 0.1% sodium azide, equilibrated against 3.0 M ammonium sulfate, VAPOR DIFFUSION, temperature 278K

Crystal Properties
Matthews coefficient	Solvent content
6.6	81.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 277.534	α = 90
b = 277.534	β = 90
c = 66.321	γ = 120

Symmetry
Space Group	H 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	77	CCD	ADSC QUANTUM 315		2004-06-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	1.00000	ALS	5.0.1

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	3.8	50	84.5	0.092	22.3	15.9	8204	8204			227

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.8	3.94	59.2		1.3	9.1	565

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1HZX	3.8	30	8168	8168	401	84.53	0.37542	0.37542	0.37333	0.41841	RANDOM	225.817

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]
-22.65	-11.33		-22.65		33.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.196
r_dihedral_angle_4_deg	20.56
r_dihedral_angle_3_deg	20.123
r_dihedral_angle_1_deg	6.009
r_angle_refined_deg	1.437
r_nbtor_refined	0.316
r_symmetry_vdw_refined	0.313
r_nbd_refined	0.244
r_symmetry_hbond_refined	0.194
r_xyhbond_nbd_refined	0.185
r_chiral_restr	0.126
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2606
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	121

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing