9LHS | pdb_00009lhs

Crystal structure of an ice-binding protein from Candidatus Cryosericum odellii

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, SITTING DROP		293	3.5 M sodium formate pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
3.47	64.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.81	α = 90
b = 66.81	β = 90
c = 142.48	γ = 90

Symmetry
Space Group	P 41 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 EIGER X 9M		2023-12-26	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)	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	1.83	29.259	100	0.06	35.2	25.7		29297

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	1.83	1.87			0.63

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	1.83	29.259	29297	1430	99.945	0.179	0.1772	0.1886	0.2094	0.2218	25.933

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]
-0.006			-0.006		0.012

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.688
r_dihedral_angle_3_deg	9.253
r_dihedral_angle_1_deg	7.115
r_dihedral_angle_4_deg	6.353
r_lrange_it	4.87
r_lrange_other	4.743
r_scangle_it	4.019
r_scangle_other	4.019
r_scbond_it	2.928
r_scbond_other	2.923
r_mcangle_other	2.474
r_mcangle_it	2.473
r_mcbond_it	1.981
r_mcbond_other	1.978
r_angle_refined_deg	1.669
r_angle_other_deg	1.468
r_nbd_refined	0.197
r_symmetry_nbd_other	0.183
r_nbtor_refined	0.156
r_nbd_other	0.136
r_xyhbond_nbd_refined	0.13
r_symmetry_xyhbond_nbd_refined	0.12
r_symmetry_nbd_refined	0.117
r_chiral_restr	0.081
r_symmetry_nbtor_other	0.079
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1570
Nucleic Acid Atoms
Solvent Atoms	215
Heterogen Atoms

Software

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