4UR6 | pdb_00004ur6

Structure of the type III fish antifreeze protein from Zoarces viviparus ZvAFP6

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OPS	PDB ENTRY 1OPS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				2.5 M (NH4)2SO4, 0.1 M CITRIC ACID, PH 4

Crystal Properties
Matthews coefficient	Solvent content
2.84	57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.57	α = 90
b = 108.17	β = 90
c = 38.25	γ = 90

Symmetry
Space Group	C 2 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	CCD	MARRESEARCH		2009-12-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-2		MAX II	I911-2

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	1.2	30	98.5	0.03	25.2	6.2		300182		-3

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	1.2	1.23	94.9		0.43	5.2	5

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1OPS	1.2	61.9	46138	2463	98.49	0.17965	0.17884	0.17	0.19536	0.19	RANDOM	24.805

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]
0.14			-0.34		0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.54
r_dihedral_angle_3_deg	10.44
r_sphericity_free	9.801
r_sphericity_bonded	7.178
r_dihedral_angle_1_deg	5.654
r_scangle_it	5.359
r_scbond_it	3.994
r_mcangle_it	2.847
r_rigid_bond_restr	2.386
r_mcbond_it	2.122
r_angle_refined_deg	1.819
r_nbtor_refined	0.31
r_symmetry_vdw_refined	0.284
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.147
r_chiral_restr	0.121
r_symmetry_hbond_refined	0.117
r_bond_refined_d	0.018
r_gen_planes_refined	0.01
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	912
Nucleic Acid Atoms
Solvent Atoms	203
Heterogen Atoms	10

Software

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