2PNE

Crystal Structure of the Snow Flea Antifreeze Protein

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BOG	PDB entry 3BOG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	296	pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
1.65	25.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 16.699	α = 90
b = 74.281	β = 102.2
c = 17.687	γ = 90

Symmetry
Space Group	P 1 21 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			2006-12-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM		APS	19-BM

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	0.95	50	90.6	0.059	17.9	3.3		23972		-3

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)
	0.95	0.98	46		0.25	3	1.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3BOG	0.98	17.29	21783	1173	95.5	0.141	0.14	0.164	RANDOM	6.59

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]
0.11		0.79	-0.79		1.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.41
r_dihedral_angle_4_deg	12.307
r_dihedral_angle_3_deg	10.983
r_sphericity_free	9.026
r_dihedral_angle_1_deg	7.229
r_sphericity_bonded	4.616
r_scangle_it	3.541
r_scbond_it	2.685
r_mcangle_it	1.938
r_angle_refined_deg	1.674
r_mcbond_it	1.429
r_rigid_bond_restr	1.34
r_mcbond_other	1.147
r_angle_other_deg	0.865
r_symmetry_vdw_other	0.212
r_nbd_refined	0.198
r_nbd_other	0.183
r_xyhbond_nbd_refined	0.183
r_nbtor_refined	0.16
r_symmetry_vdw_refined	0.156
r_symmetry_hbond_refined	0.146
r_chiral_restr	0.112
r_nbtor_other	0.083
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	453
Nucleic Acid Atoms
Solvent Atoms	113
Heterogen Atoms

Software

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