7OAQ | pdb_00007oaq

Nanobody H3 AND C1 bound to RBD with Kent mutation

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7OAP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	1.0 M Lithium chloride, 0.1 M Citrate pH 4, 20 % Peg 6000

Crystal Properties
Matthews coefficient	Solvent content
2.95	58.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.857	α = 90
b = 105.857	β = 90
c = 112.709	γ = 90

Symmetry
Space Group	P 43 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		2021-02-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9762	Diamond	I04

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	1.55	53	100	0.02	1	16.9	26.8		93033

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	1.55	1.59	93		0.59	0.6	0.6	27.6

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	7oap	1.55	52.984	92354	4722	99.27	0.156	0.155	0.17	0.1783	0.19	36.162

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]
-1.211			-1.211		2.422

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.114
r_dihedral_angle_4_deg	14.157
r_dihedral_angle_3_deg	12.225
r_rigid_bond_restr	8.608
r_dihedral_angle_1_deg	6.728
r_lrange_other	3.96
r_lrange_it	3.954
r_scangle_it	3.642
r_scangle_other	3.642
r_scbond_it	3.102
r_scbond_other	3.022
r_mcangle_other	2.776
r_mcangle_it	2.774
r_mcbond_it	2.317
r_mcbond_other	2.276
r_angle_refined_deg	1.398
r_angle_other_deg	1.34
r_symmetry_nbd_refined	0.222
r_nbd_refined	0.21
r_symmetry_nbd_other	0.183
r_xyhbond_nbd_refined	0.174
r_nbtor_refined	0.173
r_symmetry_xyhbond_nbd_refined	0.147
r_nbd_other	0.142
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.069
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3513
Nucleic Acid Atoms
Solvent Atoms	375
Heterogen Atoms	28

Software

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