9LI0 | pdb_00009li0

Crystal structure of engineered ice-binding protein (M74I and A97V) from Candidatus Cryosericum odellii strain SMC5_169

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9LHN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	90% of precipitant (35% PEG 2000 MME), 10% of mixture(6 M Ammonium nitrate, 0.1M Tris pH 8.5)

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.15	α = 90
b = 61.92	β = 94.26
c = 92.54	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	PIXEL	DECTRIS EIGER X 9M		2024-05-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 5C (4A)	1	PAL/PLS	5C (4A)

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	1.453	29.352	99.51	0.03924	0.01636	0.999	28.83	6.6		61537

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	1.453	1.505	96.95		0.1599	0.07278	0.988	8.53	5.6

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.453	29.352	61537	3077	99.521	0.155	0.1535	0.1535	0.1816	0.1815	10.438

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]
0.001		-0.001	-0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.501
r_dihedral_angle_4_deg	15.454
r_dihedral_angle_3_deg	9.617
r_dihedral_angle_1_deg	7.545
r_lrange_it	3.529
r_lrange_other	3.313
r_scangle_other	2.258
r_scangle_it	2.256
r_angle_refined_deg	1.839
r_scbond_it	1.607
r_angle_other_deg	1.602
r_scbond_other	1.601
r_mcangle_it	1.357
r_mcangle_other	1.357
r_mcbond_it	0.951
r_mcbond_other	0.951
r_symmetry_nbd_refined	0.291
r_nbd_refined	0.212
r_nbd_other	0.211
r_symmetry_nbd_other	0.191
r_symmetry_xyhbond_nbd_refined	0.168
r_nbtor_refined	0.164
r_xyhbond_nbd_refined	0.114
r_chiral_restr	0.093
r_symmetry_nbtor_other	0.088
r_bond_refined_d	0.014
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3117
Nucleic Acid Atoms
Solvent Atoms	482
Heterogen Atoms

Software

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