7Z1E | pdb_00007z1e

Nanobody H11-H4 Q98R H100E 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	0.2M Ammonium nitrate, 20 % Peg 3350

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.243	α = 90
b = 78.243	β = 90
c = 126.812	γ = 120

Symmetry
Space Group	P 31 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 EIGER2 XE 16M		2021-07-14	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	1.59	67.761	100	0.046	0.999	24.9	18.8		61104

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	1.59	1.62	100		4.156	0.361	0.4	20.2

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	1.59	67.761	61035	3095	99.972	0.163	0.161	0.17	0.2023	0.21	38.799

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]
-0.473	-0.237		-0.473		1.535

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.597
r_dihedral_angle_4_deg	15.032
r_dihedral_angle_3_deg	11.691
r_dihedral_angle_1_deg	6.994
r_lrange_other	4.131
r_lrange_it	4.128
r_scangle_it	3.287
r_scangle_other	3.237
r_mcangle_other	3.055
r_mcangle_it	3.05
r_scbond_it	2.621
r_scbond_other	2.527
r_mcbond_it	2.307
r_mcbond_other	2.293
r_rigid_bond_restr	1.36
r_angle_refined_deg	1.306
r_angle_other_deg	1.267
r_symmetry_nbd_refined	0.266
r_nbd_other	0.215
r_nbd_refined	0.186
r_symmetry_nbd_other	0.178
r_nbtor_refined	0.171
r_symmetry_xyhbond_nbd_refined	0.147
r_xyhbond_nbd_refined	0.123
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.061
r_bond_refined_d	0.005
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	2520
Nucleic Acid Atoms
Solvent Atoms	206
Heterogen Atoms	40

Software

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