3UYV | pdb_00003uyv

Crystal structure of a glycosylated ice-binding protein (LeIBP) from Arctic yeast

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	292	0.1M imidazole, pH 8.5, 1. M potassium phosphate, 0.5M sodium phosphate, 0.2M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.64	α = 90
b = 58.64	β = 90
c = 292.641	γ = 120

Symmetry
Space Group	P 65 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	200	IMAGE PLATE	RIGAKU RAXIS IV++		2011-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54180

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.43	50.78	93.8			11886	11149	1	1

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	2.43	2.56	99.5

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	3UYU	2.43	50.78	11149	10549	533	91.22	0.23656	0.23587	0.23338	0.24	0.28617	0.28	RANDOM	23.596

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]
-0.01	-0.01		-0.01		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.201
r_dihedral_angle_3_deg	17.298
r_dihedral_angle_4_deg	8.782
r_dihedral_angle_1_deg	6.821
r_scangle_it	3.338
r_angle_refined_deg	2.208
r_scbond_it	2.054
r_mcangle_it	1.439
r_mcbond_it	0.793
r_chiral_restr	0.114

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.201
r_dihedral_angle_3_deg	17.298
r_dihedral_angle_4_deg	8.782
r_dihedral_angle_1_deg	6.821
r_scangle_it	3.338
r_angle_refined_deg	2.208
r_scbond_it	2.054
r_mcangle_it	1.439
r_mcbond_it	0.793
r_chiral_restr	0.114
r_bond_refined_d	0.018
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1674
Nucleic Acid Atoms
Solvent Atoms	14
Heterogen Atoms	50

Software

Software
Software Name	Purpose
PROTEUM PLUS	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.