7BWX

Crystal structure of ice-binding protein from an Antarctic ascomycete, Antarctomyces psychrotrophicus.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3WP9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.6	293	0.1 M HEPES-NaOH pH 8.6, 0.95 M ammonium sulfate and 0.1 M lithium sulfate

Crystal Properties
Matthews coefficient	Solvent content
3.38	64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.427	α = 90
b = 207.281	β = 90
c = 100.784	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 S 6M		2016-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	0.9800	Photon Factory	BL-17A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	1.9	47.62	99.9	0.107	0.045	0.997	12.9	6.7		141990			15.45

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2.01	99.6		0.467	0.197	0.888	4.2	6.6

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3WP9	1.904	47.62	141916	7119	99.889	0.137	0.1366	0.1351	0.1641	Random selection	19.482

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]
-0.481			0.916		-0.435

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.994
r_dihedral_angle_3_deg	10.629
r_dihedral_angle_1_deg	7.204
r_lrange_it	6.661
r_lrange_other	6.147
r_scangle_it	4.535
r_scangle_other	4.534
r_dihedral_angle_4_deg	3.676
r_scbond_it	3.075
r_scbond_other	3.074
r_mcangle_it	2.959
r_mcangle_other	2.959
r_mcbond_it	1.951
r_mcbond_other	1.947
r_angle_refined_deg	1.695
r_angle_other_deg	1.538
r_symmetry_xyhbond_nbd_refined	0.23
r_nbd_refined	0.204
r_symmetry_nbd_other	0.179
r_xyhbond_nbd_refined	0.176
r_nbtor_refined	0.159
r_symmetry_nbd_refined	0.14
r_nbd_other	0.099
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.076
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8442
Nucleic Acid Atoms
Solvent Atoms	1534
Heterogen Atoms	72

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing