8OP0 | pdb_00008op0

VHH Z70 mutant 20 in interaction with PHF6 Tau peptide

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	293	0.095M tri-Sodium citrate pH 5.6, 19% isopropanol, 15% Glycerol

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.309	α = 90
b = 135.309	β = 90
c = 35.508	γ = 120

Symmetry
Space Group	P 65 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 16M		2023-03-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.9786	SOLEIL	PROXIMA 1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.54	44.29	97.5	0.071	0.072	0.015	0.999	31.5	40.8		28067

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.54	1.57			1.788	1.83	0.385	0.881		42.8

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	1.54	44.23	28067	1403	97.195	0.162	0.1598	0.17	0.1967	0.21	28.861

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]
0.003	0.001		0.003		-0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.805
r_dihedral_angle_3_deg	14.487
r_dihedral_angle_2_deg	7.316
r_dihedral_angle_1_deg	7.135
r_rigid_bond_restr	5.897
r_lrange_it	4.93
r_lrange_other	4.723
r_scangle_other	3.915
r_scangle_it	3.913
r_mcangle_other	3.72
r_mcangle_it	3.719
r_scbond_it	3.188
r_scbond_other	3.186
r_mcbond_other	2.877
r_mcbond_it	2.876
r_angle_refined_deg	1.575
r_angle_other_deg	0.547
r_symmetry_nbd_refined	0.323
r_nbd_other	0.231
r_nbd_refined	0.224
r_symmetry_nbd_other	0.196
r_symmetry_xyhbond_nbd_refined	0.196
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.142
r_symmetry_nbtor_other	0.089
r_chiral_restr	0.082
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	938
Nucleic Acid Atoms
Solvent Atoms	94
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Coot	model building
XDS	data reduction
Aimless	data scaling
MOLREP	phasing