8P6H | pdb_00008p6h

Bovine naive ultralong antibody AbBLV5B8* 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	4K3D
experimental model	PDB	6QN7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	10% w/v PEG 20000, 20% v/v PEG MME 550, 0.02M Sodium L-glutamate, 0.02M DL-Alanine, 0.02M Glycine, 0.02M DL-Lysine HCl, 0.02M DL-Serine, 0.1 M MOPS/HEPES-Na

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 161.16	α = 90
b = 49.045	β = 90.87
c = 60.381	γ = 90

Symmetry
Space Group	C 1 2 1

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 microred aperture, horizontally and vertically focussing 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	1.46	80.57	100	0.07	0.076	0.029	0.999	12	6.6		82095

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	1.46	1.49		100	1.825	2.019	0.847	0.365		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	1.46	80.57	78110	3984	99.99	0.22379	0.22186	0.23	0.26109	0.27	RANDOM	29.799

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]
-1.01		0.22	1.4		-0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.69
r_long_range_B_refined	7.933
r_long_range_B_other	7.933
r_dihedral_angle_1_deg	7.672
r_dihedral_angle_2_deg	7.25
r_scangle_other	5.371
r_mcangle_it	4.779
r_mcangle_other	4.778
r_scbond_it	3.547
r_scbond_other	3.546
r_mcbond_it	3.289
r_mcbond_other	3.283
r_angle_refined_deg	1.528
r_angle_other_deg	0.532
r_chiral_restr	0.073
r_gen_planes_refined	0.009
r_bond_refined_d	0.008
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3165
Nucleic Acid Atoms
Solvent Atoms	290
Heterogen Atoms

Software

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