2I36 | pdb_00002i36

Crystal structure of trigonal crystal form of ground-state rhodopsin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HZX	PDB entry 1HZX

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
4.5	72.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 159.866	α = 90
b = 159.866	β = 90
c = 142.15	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	77	CCD	ADSC QUANTUM 315		2004-04-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.97970	SSRL	BL11-1

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	4	50	99.7	0.087	21.1	10.6	17705	17705			185

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	4	4.15	100

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 1HZX	4.1	30	16375	16375	832	99.82	0.38367	0.38367	0.38229	0.38	0.41153	0.41	RANDOM	185

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]
-13.16	-6.58		-13.16		19.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.202
r_dihedral_angle_3_deg	21.531
r_dihedral_angle_4_deg	17.059
r_dihedral_angle_1_deg	6.376
r_angle_refined_deg	1.327
r_symmetry_vdw_refined	0.342
r_nbtor_refined	0.316
r_nbd_refined	0.23
r_symmetry_hbond_refined	0.17
r_xyhbond_nbd_refined	0.169
r_chiral_restr	0.084
r_bond_refined_d	0.011
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	7665
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	218

Software

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