7A6O

Crystal Structure of the Complex of the Recombinant Von Willebrand Factor AIM-A1 domain and VHH81 at 2.1 Angstrom resolution

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AUQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.2	283	3.2 M ammonium sulphate, 0.08 M sodium citrate

Crystal Properties
Matthews coefficient	Solvent content
3.32	62.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.234	α = 90
b = 65.234	β = 90
c = 233.231	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	283	PIXEL	DECTRIS EIGER2 XE 16M		2020-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	2.117	62.9	92.4	0.048	1	15.1	5.2		19344

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	2.117	2.3	69.2		0.645	0.6	1.7

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	1AUQ	2.117	62.8	19344	921	92.4	0.198	0.1947	0.21	0.2558	0.26	51.291

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]
-0.155			-0.155		0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.913
r_lrange_other	24.864
r_lrange_it	24.822
r_dihedral_angle_4_deg	20.867
r_dihedral_angle_3_deg	16.499
r_scangle_it	7.914
r_scangle_other	7.88
r_dihedral_angle_1_deg	7.55
r_mcangle_it	5.937
r_mcangle_other	5.935
r_scbond_it	5.244
r_scbond_other	5.211
r_mcbond_it	4.265
r_mcbond_other	4.265
r_angle_other_deg	2.339
r_angle_refined_deg	1.727
r_symmetry_nbd_refined	0.569
r_symmetry_xyhbond_nbd_refined	0.387
r_xyhbond_nbd_other	0.278
r_symmetry_nbd_other	0.22
r_nbd_refined	0.211
r_xyhbond_nbd_refined	0.191
r_nbtor_refined	0.162
r_nbd_other	0.154
r_symmetry_xyhbond_nbd_other	0.133
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.07
r_bond_other_d	0.035
r_gen_planes_other	0.011
r_bond_refined_d	0.01
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2620
Nucleic Acid Atoms
Solvent Atoms	160
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHENIX	phasing