8XLD | pdb_00008xld

Structure of the GFP:GFP-nanobody complex from Biortus.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold
experimental model	PDB	7D30

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2M Na2SO4, 0.1M Bis-Tris propane pH6.5, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.544	α = 90
b = 88.363	β = 90
c = 122.842	γ = 90

Symmetry
Space Group	I 2 2 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 EIGER X 9M		2023-08-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.953729	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.1	44.221	100	0.166	11.5	13.4		25324

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.16			1.083

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.1	44.221	25322	1267	99.964	0.165	0.1623	0.1732	0.2092	0.2223	35.475

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]
2.096			1.094		-3.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.995
r_dihedral_angle_3_deg	12.519
r_lrange_other	8.54
r_lrange_it	8.524
r_dihedral_angle_1_deg	7.499
r_dihedral_angle_2_deg	7.09
r_scangle_it	6.254
r_scangle_other	6.252
r_mcangle_it	4.794
r_mcangle_other	4.793
r_scbond_it	4.016
r_scbond_other	4.015
r_mcbond_it	3.105
r_mcbond_other	3.103
r_angle_refined_deg	1.454
r_angle_other_deg	0.491
r_symmetry_nbd_refined	0.223
r_symmetry_nbd_other	0.198
r_nbd_refined	0.193
r_nbd_other	0.185
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.176
r_symmetry_xyhbond_nbd_refined	0.104
r_symmetry_nbtor_other	0.091
r_chiral_restr	0.065
r_gen_planes_refined	0.007
r_bond_refined_d	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2630
Nucleic Acid Atoms
Solvent Atoms	247
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing