7OAP | pdb_00007oap

Nanobody H3 AND C1 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, SITTING DROP		293	1.0 M Lithium chloride, 0.1 M Citrate pH 4, 20 % Peg 6000

Crystal Properties
Matthews coefficient	Solvent content
2.94	58.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.683	α = 90
b = 105.683	β = 90
c = 112.539	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		2020-09-16	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	1.9	62.254	100	0.025	0.99	14.4	25.4		50645

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.95	100		0.94	0.7	22.1

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	1.901	62.254	50645	2656	99.923	0.182	0.1802	0.19	0.204	0.21	44.25

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]
0.759			0.759		-1.518

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.989
r_dihedral_angle_4_deg	14.764
r_dihedral_angle_3_deg	13.46
r_dihedral_angle_1_deg	7.375
r_lrange_other	7.254
r_lrange_it	7.253
r_scangle_it	4.978
r_scangle_other	4.977
r_scbond_it	3.37
r_scbond_other	3.194
r_mcangle_other	2.938
r_mcangle_it	2.937
r_mcbond_it	2.04
r_mcbond_other	2.036
r_angle_refined_deg	1.528
r_angle_other_deg	1.342
r_symmetry_nbd_refined	0.235
r_nbd_other	0.22
r_nbd_refined	0.192
r_symmetry_nbd_other	0.175
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.146
r_symmetry_xyhbond_nbd_refined	0.135
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.068
r_symmetry_xyhbond_nbd_other	0.04
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3509
Nucleic Acid Atoms
Solvent Atoms	235
Heterogen Atoms	28

Software

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