8P2T | pdb_00008p2t

Bovine naive ultralong antibody AbD08* collected at 100K

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8BS8
experimental model	PDB	6QN7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.03M Sodium Fluoride, 0.03M Sodium Bromide, 0.03M Sodium Iodide, 0.1 M MOPS/HEPES-Na

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.03	α = 90
b = 70.86	β = 90
c = 96.01	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	100	PIXEL	DECTRIS EIGER X 16M	130x80 microrad aperture, horizontally and vertically focusing mirrors, 4xslits, variable focus beam	2020-02-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.45	39.74	100	0.07	0.076	0.03	0.999	10.4	6.6		79276

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.47		100	2.604	2.868	1.189	0.325		5.7

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	1.45	39.74	75241	3958	99.96	0.15057	0.14766	0.15	0.20555	0.21	RANDOM	24.128

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]
1.53			0.42		-1.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	11.895
r_dihedral_angle_1_deg	7.932
r_rigid_bond_restr	5.463
r_dihedral_angle_2_deg	4.776
r_long_range_B_refined	3.974
r_long_range_B_other	3.973
r_scangle_other	2.955
r_mcangle_it	2.781
r_mcangle_other	2.781
r_scbond_it	2.363
r_scbond_other	2.363
r_mcbond_it	2.31
r_mcbond_other	2.31
r_angle_refined_deg	1.639
r_angle_other_deg	0.596
r_chiral_restr	0.09
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
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_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3507
Nucleic Acid Atoms
Solvent Atoms	539
Heterogen Atoms	9

Software

Software
Software Name	Purpose
REFMAC	refinement
pointless	data scaling
xia2	data reduction
PHASER	phasing