9LHN | pdb_00009lhn

Crystal structure of Ice binding protein from Candidatus Cryosericum odellii SMC5

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4NU2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	35% (w/v) PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.02	38.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.33	α = 90
b = 62.14	β = 93.746
c = 93.62	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		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	1.45	29.5	99.2	0.08	16.5	6.9		62809

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	1.45	1.53	99.2		0.32	6.5

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	1.45	29.5	62809	3124	98.764	0.152	0.1505	0.1505	0.1775	0.1773	8.967

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

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.748
r_dihedral_angle_4_deg	20.134
r_dihedral_angle_3_deg	9.534
r_dihedral_angle_1_deg	7.315
r_lrange_it	3.586
r_lrange_other	3.411
r_scangle_other	2.297
r_scangle_it	2.296
r_angle_refined_deg	1.781
r_scbond_it	1.707
r_scbond_other	1.705
r_angle_other_deg	1.569
r_mcangle_it	1.374
r_mcangle_other	1.374
r_mcbond_it	0.911
r_mcbond_other	0.911
r_symmetry_nbd_refined	0.265
r_nbd_refined	0.213
r_symmetry_nbd_other	0.188
r_nbtor_refined	0.161
r_symmetry_xyhbond_nbd_refined	0.13
r_nbd_other	0.127
r_xyhbond_nbd_refined	0.121
r_chiral_restr	0.087
r_symmetry_nbtor_other	0.085
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3131
Nucleic Acid Atoms
Solvent Atoms	523
Heterogen Atoms

Software

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