6W78 | pdb_00006w78

crystal structure of a plant ice-binding protein

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OGQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	291	0.2 M sodium malonate (pH 4.0), and 20% w/v polyethylene glycol 3,350

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.895	α = 90
b = 57.453	β = 90
c = 135.538	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	MAR CCD 165 mm		2017-10-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.978	SSRF	BL17U

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	2.3	50	99.8	0.127	18	8.8		13160

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)
1	2.3	2.36			0.491

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1OGQ	2.311	37.414	13848	688	99.39	0.165	0.1622	0.17	0.2228	0.18	38.373

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]
0.107			-1.166		1.058

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.238
r_dihedral_angle_4_deg	21.527
r_dihedral_angle_3_deg	16.941
r_dihedral_angle_1_deg	7.722
r_lrange_other	5.642
r_lrange_it	5.64
r_scangle_it	4.314
r_scangle_other	4.313
r_scbond_it	2.755
r_scbond_other	2.755
r_mcangle_it	2.483
r_mcangle_other	2.482
r_angle_refined_deg	2.047
r_mcbond_it	1.66
r_mcbond_other	1.659
r_angle_other_deg	1.371
r_symmetry_nbd_refined	0.266
r_symmetry_xyhbond_nbd_refined	0.243
r_nbd_other	0.233
r_nbd_refined	0.208
r_symmetry_nbd_other	0.196
r_xyhbond_nbd_refined	0.192
r_nbtor_refined	0.171
r_symmetry_xyhbond_nbd_other	0.142
r_xyhbond_nbd_other	0.126
r_chiral_restr	0.09
r_symmetry_nbtor_other	0.088
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2413
Nucleic Acid Atoms
Solvent Atoms	114
Heterogen Atoms	28

Software

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