3DBA

Crystal structure of the cGMP-bound GAF a domain from the photoreceptor phosphodiesterase 6C

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	295	1.5 M ammonium sulfate, 0.1 M sodium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.598	α = 90
b = 67.598	β = 90
c = 198.533	γ = 120

Symmetry
Space Group	P 32 2 1

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	ADSC QUANTUM 4r		2006-08-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A	0.97912	NSLS	X4A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.57	43.85	99.1	0.074	51.8	10.2	17389	17389		-3	57

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.57	2.66	100		56.5	4.8	9.4	1715

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.57	43.85	17389	17159	860	98.15	0.22245	0.22063	0.25705	RANDOM	68.876

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]
7.33	3.67		7.33		-11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.161
r_dihedral_angle_3_deg	17.936
r_dihedral_angle_4_deg	15.664
r_dihedral_angle_1_deg	6.946
r_mcangle_it	3.907
r_scangle_it	3.623
r_mcbond_it	3.075
r_scbond_it	2.752
r_angle_refined_deg	1.259
r_angle_other_deg	0.813
r_mcbond_other	0.768
r_symmetry_vdw_refined	0.26
r_symmetry_vdw_other	0.244
r_symmetry_hbond_refined	0.226
r_nbd_refined	0.216
r_nbd_other	0.181
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.154
r_nbtor_other	0.083
r_chiral_restr	0.069
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2736
Nucleic Acid Atoms
Solvent Atoms	79
Heterogen Atoms	76

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing