Experiment: 4C2B

Crystal Structure of High-Affinity von Willebrand Factor A1 domain with Disulfide Mutation in Complex with High Affinity GPIb alpha

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4C2A	PDB ENTRY 4C2A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.6		CRYSTALS OF A1/SS-GPIB/VWD2 COMPLEX APPEARED IN DROPS WITH 20% PEG 4000, 0.16 M AMMONIUM SULFATE, 0.08M SODIUM ACETATE, PH 4.6, AND 20% GLYCEROL. THESE CRYSTALS WERE CRUSHED AND USED FOR SEEDING CRYSTAL GROWTH IN 8 MG/ML COMPLEX, 15% PEG 4000, 0.16 M AMMONIUM SULFATE, 0.08 M SODIUM ACETATE, PH 4.6, AND 20% GLYCEROL. SINCE THESE CRYSTALS WERE FORMED IN BUFFER CONTAINING 20% GLYCEROL, NO ADDITIONAL CRYOPROTECTION WAS USED.

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.53	α = 90
b = 103.84	β = 90.05
c = 119.93	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	CCD	MARRESEARCH MX-300		2013-04-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID		APS	22-ID

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	2.8	48.3	96.6	0.59	2.56	2.5		56526		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.87	80.9		0.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 4C2A	2.8	48.265	2	56511	1478	96.6	0.2566	0.2527	0.2542	0.2859

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	8.671
f_angle_d	0.465
f_chiral_restr	0.031
f_bond_d	0.002
f_plane_restr	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14634
Nucleic Acid Atoms
Solvent Atoms	65
Heterogen Atoms	69

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALEPACK	data scaling