6XNR | pdb_00006xnr

Crystal structure of Rhagium Mordax antifreeze protein

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4DT5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	295	PEG monomethyl ether 5000, sodium acetate, magnesium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.457	α = 90
b = 91.143	β = 90
c = 117.447	γ = 90

Symmetry
Space Group	P 21 2 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	PIXEL	DECTRIS PILATUS3 S 6M		2018-03-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.9795	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.05	50	99.7	0.068	0.998	9	13.3		45419

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.11	99.4		0.519	0.835	2	13.7

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	THROUGHOUT	4DT5	2.05	49.413	45380	2230	99.666	0.215	0.2131	0.22	0.2509	0.25	32.012

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]
-3.624			1.162		2.463

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.032
r_dihedral_angle_4_deg	23.754
r_dihedral_angle_3_deg	11.898
r_lrange_other	9.66
r_lrange_it	9.633
r_dihedral_angle_1_deg	6.32
r_angle_other_deg	1.516
r_angle_refined_deg	1.471
r_mcangle_it	1.071
r_mcangle_other	1.071
r_scangle_it	0.677
r_scangle_other	0.677
r_mcbond_it	0.581
r_mcbond_other	0.581
r_scbond_other	0.417
r_scbond_it	0.412
r_symmetry_nbd_refined	0.272
r_nbd_other	0.25
r_symmetry_nbd_other	0.214
r_nbd_refined	0.173
r_xyhbond_nbd_refined	0.166
r_symmetry_xyhbond_nbd_refined	0.147
r_nbtor_refined	0.127
r_ncsr_local_group_5	0.103
r_ncsr_local_group_2	0.099
r_ncsr_local_group_3	0.097
r_ncsr_local_group_1	0.096
r_ncsr_local_group_9	0.096
r_ncsr_local_group_4	0.093
r_ncsr_local_group_7	0.09
r_ncsr_local_group_6	0.086
r_ncsr_local_group_8	0.084
r_symmetry_nbtor_other	0.082
r_ncsr_local_group_10	0.074
r_chiral_restr	0.054
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4393
Nucleic Acid Atoms
Solvent Atoms	514
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing