8CIF | pdb_00008cif

Bovine naive ultralong antibody AbD08 collected at 293K

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8BS8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.1M Tris (base) 0.1M Bicine 12% (v/v) PEG 500 MME 6% (v/v) PEG 20000 0.15M Sodium chloride 0.09M Sodium fluoride 0.09M Sodium iodide 0.09M Sodium bromide
2	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.1M Tris (base) 0.1M Bicine 12% (v/v) PEG 500 MME 6% (v/v) PEG 20000 0.15M Sodium chloride 0.09M Sodium nitrate 0.09M Sodium phosphate dibasic 0.09M Ammonium sulphate
3	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.1M Tris (base) 0.1M Bicine 12% (v/v) PEG 500 MME 6% (v/v) PEG 20000 0.15M Sodium chloride 0.09M Sodium nitrate 0.09M Sodium phosphate dibasic 0.09M Ammonium sulphate
4	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.1M Tris (base) 0.1M Bicine 12% (v/v) PEG 500 MME 6% (v/v) PEG 20000 0.15M Sodium chloride 0.1M Sodium formate 0.1M Ammonium Acetate 0.1M Sodium citrate tribasic dihydrate 0.1M Potassium sodium tartrate tetrahydrate 0.1M Sodium oxamate

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.29
1.99	38.29
1.99	38.29
1.99	38.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.228	α = 90
b = 71.585	β = 90
c = 100.233	γ = 90

Symmetry
Space Group	P 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	293	PIXEL	DECTRIS EIGER2 X 4M	130x80 microrad aperture, horizontally and vertically focusing mirrors, 4xslits, variable microfocus beam	2019-12-02	M	SINGLE WAVELENGTH
2	2	x-ray	293	PIXEL	DECTRIS EIGER2 X 4M	130x80 microrad aperture, horizontally and vertically focusing mirrors, 4xslits, variable microfocus beam	2019-12-02	M	SINGLE WAVELENGTH
3	3	x-ray	293	PIXEL	DECTRIS EIGER2 X 4M	130x80 microrad aperture, horizontally and vertically focusing mirrors, 4xslits, variable microfocus beam	2019-12-02	M	SINGLE WAVELENGTH
4	4	x-ray	293	PIXEL	DECTRIS EIGER2 X 4M	130x80 microrad aperture, horizontally and vertically focusing mirrors, 4xslits, variable microfocus beam	2019-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE VMXi	0.9795	Diamond	VMXi
2	SYNCHROTRON	DIAMOND BEAMLINE VMXi	0.9795	Diamond	VMXi
3	SYNCHROTRON	DIAMOND BEAMLINE VMXi	0.9795	Diamond	VMXi
4	SYNCHROTRON	DIAMOND BEAMLINE VMXi	0.9795	Diamond	VMXi

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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
2	2.07	58.27	76	0.103	1	6	1.9		21940

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
2	2.07	2.11			0.831	0.5	0.5

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 (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	2.2	58.32	21885	1127	95.45	0.17963	0.17713	0.18	0.22786	0.24	RANDOM	36.51

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]
-0.07			0.02		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.732
r_dihedral_angle_4_deg	14.589
r_dihedral_angle_3_deg	13.898
r_dihedral_angle_1_deg	8.295
r_long_range_B_refined	7.671
r_long_range_B_other	7.665
r_scangle_other	5.46
r_mcangle_it	4.691
r_mcangle_other	4.69
r_scbond_it	3.564
r_scbond_other	3.555
r_mcbond_it	3.059
r_mcbond_other	3.047
r_angle_refined_deg	1.522
r_angle_other_deg	1.3
r_chiral_restr	0.065
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3415
Nucleic Acid Atoms
Solvent Atoms	52
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data scaling
DIALS	data reduction
PHASER	phasing