2IFU | pdb_00002ifu

Crystal Structure of a Gamma-SNAP from Danio rerio

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	Protein Solution (10 MG/ML protein, 0.250 M sodium chloride, 0.0031 M sodium azide, 0.0003 M TCEP, 0.005 M BisTris pH 7.0) mixed in a 1:1 ratio with the Well Solution (15% PEG 8K, 0.020 M lithium sulfate, 0.066 M PIPES pH 6.5, 0.034 M MOPS pH 7.0) Cryoprotected with Well Solution supplemented with up to 25% ethylene glycol, vapor diffusion, hanging drop, temperature 277K
2	VAPOR DIFFUSION, HANGING DROP		277	Protein Solution (10 MG/ML protein, 0.250 M sodium chloride, 0.0031 M sodium azide, 0.0003 M TCEP, 0.005 M BisTris pH 7.0) mixed in a 1:1 ratio with the Well Solution (7% PEG 8K, 0.20 M ammonium sulfate, 0.10 M MOPS pH 7) Cryoprotected with 15% PEG 8K, 0.100 M lithium sulfate, 0.10 M PIPES pH 6.5 up to 25% ethylene glycol, vapor diffusion, hanging drop, temperature 277K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.378	α = 90
b = 90.813	β = 90
c = 264.173	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARMOSAIC 300 mm CCD	Adjustable focusing mirrors in K-B geometry	2006-08-24	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD	Horizontal sagitally focusing 2nd bent monochromator crystal, vertical bent focusing mirror	2006-08-04	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97926	APS	23-ID-D
2	SYNCHROTRON	APS BEAMLINE 22-ID	0.97925,0.96403	APS	22-ID

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
1,2	2.4	40.053	88.3	0.093	11.759	9.8		70210

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)
	2.4	2.46	53.4		0.568	1.19	3.4	2812

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.6	40.053	60191	3047	96.072	0.24	0.239	0.261	RANDOM	70.106

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]
-1.692			2.414		-0.722

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.4
r_dihedral_angle_3_deg	19.433
r_dihedral_angle_4_deg	17.797
r_dihedral_angle_1_deg	5.507
r_scangle_it	3.223
r_scbond_it	1.998
r_angle_refined_deg	1.469
r_mcangle_it	1.184
r_mcbond_it	0.707
r_symmetry_vdw_refined	0.319
r_nbtor_refined	0.31
r_symmetry_hbond_refined	0.249
r_nbd_refined	0.228
r_xyhbond_nbd_refined	0.143
r_chiral_restr	0.1
r_bond_refined_d	0.017
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8644
Nucleic Acid Atoms
Solvent Atoms	64
Heterogen Atoms	50

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing
SHELXD	phasing