7OAO | pdb_00007oao

Nanobody C5 bound to RBD

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6ZBP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	0.2 M Sodium Acetate, 0.1 M Sodium Cacodylate pH 6.5, 30 % w/v PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.22	α = 90
b = 154.33	β = 90
c = 28.82	γ = 90

Symmetry
Space Group	P 21 21 2

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 PILATUS 6M		2020-07-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.5	51.443	99.4	0.013	1	28.1	11.8		51783

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.54	93.7		0.15	0.96	6

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6ZBP	1.5	51.443	51782	2555	99.351	0.154	0.1521	0.15	0.186	0.19	25.667

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]
2.782			-2.664		-0.118

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.572
r_dihedral_angle_4_deg	16.935
r_dihedral_angle_3_deg	11.178
r_dihedral_angle_1_deg	6.983
r_lrange_other	3.21
r_lrange_it	3.205
r_scangle_it	2.18
r_scangle_other	2.18
r_mcangle_other	2.046
r_mcangle_it	2.044
r_rigid_bond_restr	1.856
r_scbond_it	1.711
r_scbond_other	1.711
r_mcbond_it	1.579
r_mcbond_other	1.57
r_angle_refined_deg	1.443
r_angle_other_deg	1.388
r_symmetry_nbd_refined	0.26
r_symmetry_xyhbond_nbd_refined	0.235
r_xyhbond_nbd_refined	0.23
r_nbd_other	0.23
r_nbd_refined	0.197
r_symmetry_nbd_other	0.176
r_nbtor_refined	0.171
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.065
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2452
Nucleic Acid Atoms
Solvent Atoms	290
Heterogen Atoms	18

Software

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