1VES | pdb_00001ves

Structure of New Antigen Receptor variable domain from sharks

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VER	12Y-1 VNAR PDB ENTRY 1VER

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	298	0.1M Sodium citrate, 20% v/v iso-Propanol, 20% PEG4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.94	58.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.283	α = 90
b = 92.046	β = 90
c = 98.224	γ = 90

Symmetry
Space Group	I 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	113	IMAGE PLATE	MAR scanner 180 mm plate	AXCO MICROCAPILLARY FOCUSING OPTICS	2003-10-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.18	18.12	100	0.054	0.054	32.5	6.6		14981

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.18	2.24	99.4		4	6.3

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-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	12Y-1 VNAR PDB ENTRY 1VER	2.18	18.12	14981	783	99.87	0.17912	0.17912	0.17574	0.18	0.24721	0.25	RANDOM	21.292

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]
-1.07			0.07		1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.648
r_scangle_it	3.05
r_scbond_it	1.826
r_angle_refined_deg	1.484
r_mcangle_it	1.14
r_angle_other_deg	0.868
r_mcbond_it	0.591
r_nbd_other	0.251
r_symmetry_vdw_other	0.251
r_symmetry_vdw_refined	0.208
r_symmetry_hbond_refined	0.199
r_nbd_refined	0.193
r_xyhbond_nbd_refined	0.188
r_chiral_restr	0.101
r_nbtor_other	0.086
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1762
Nucleic Acid Atoms
Solvent Atoms	358
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CCP4	model building
REFMAC	refinement
MOLREP	phasing