9LHR | pdb_00009lhr

Crystal structure of Ice binding protein from Candidatus Cryosericum odellii SMC5

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	0.1 M sodium cacodylate pH 5.0, 0.2 M Sodium acetate trihydrate

Crystal Properties
Matthews coefficient	Solvent content
2.32	47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 219.75	α = 90
b = 47.56	β = 92.222
c = 66.77	γ = 90

Symmetry
Space Group	C 1 2 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		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	1.8	29.394	98.6	0.04	25.6	6.9		63299

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	1.8	1.84			0.18

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	1.8	29.394	63298	3189	98.293	0.165	0.1631	0.1743	0.2051	0.2131	17.116

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]
0.002		-0.003	-0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.706
r_dihedral_angle_4_deg	15.4
r_dihedral_angle_3_deg	10.077
r_dihedral_angle_1_deg	7.398
r_lrange_it	4.142
r_lrange_other	3.897
r_scangle_it	2.777
r_scangle_other	2.776
r_scbond_it	1.871
r_scbond_other	1.871
r_mcangle_it	1.834
r_mcangle_other	1.834
r_angle_refined_deg	1.674
r_angle_other_deg	1.433
r_mcbond_it	1.374
r_mcbond_other	1.363
r_symmetry_nbd_other	0.191
r_nbd_refined	0.189
r_symmetry_nbd_refined	0.159
r_nbtor_refined	0.157
r_nbd_other	0.15
r_xyhbond_nbd_refined	0.132
r_symmetry_xyhbond_nbd_refined	0.108
r_chiral_restr	0.084
r_symmetry_nbtor_other	0.082
r_bond_refined_d	0.011
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	4802
Nucleic Acid Atoms
Solvent Atoms	760
Heterogen Atoms

Software

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