7Z1D | pdb_00007z1d

Nanobody H11-H6 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	0.1 M HEPES, pH 7.5 and 20% w/v PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.41	α = 90
b = 65.08	β = 90
c = 82.9	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 PILATUS 6M		2020-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	45.04	98.5	0.083	0.999	18.3	13.5		48875

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.59	97.1		1.243	0.746	2.2	13.2

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	THROUGHOUT	6ZBP	1.55	45.04	48825	2359	98.271	0.168	0.1667	0.18	0.1862	0.2	21.494

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]
-0.587			0.193		0.395

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.213
r_dihedral_angle_4_deg	14.261
r_dihedral_angle_1_deg	13.735
r_dihedral_angle_3_deg	11.952
r_lrange_it	6.441
r_lrange_other	6.44
r_dihedral_angle_other_3_deg	5.575
r_scangle_it	5.125
r_scangle_other	5.124
r_scbond_it	3.398
r_scbond_other	3.397
r_mcangle_other	2.955
r_mcangle_it	2.949
r_mcbond_it	2.038
r_mcbond_other	2.022
r_angle_other_deg	1.357
r_angle_refined_deg	1.315
r_nbd_other	0.243
r_symmetry_xyhbond_nbd_refined	0.234
r_symmetry_nbd_refined	0.208
r_nbd_refined	0.189
r_symmetry_nbd_other	0.179
r_nbtor_refined	0.174
r_xyhbond_nbd_refined	0.137
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.066
r_xyhbond_nbd_other	0.028
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2525
Nucleic Acid Atoms
Solvent Atoms	312
Heterogen Atoms	20

Software

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