Experiment: 7VHD

Crystal structure of the STX2a complexed with R4A peptide

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7D6R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	4 M Sodium Formate, 100mM MES pH 6.5, 50 mM PPS

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 146.41	α = 90
b = 146.41	β = 90
c = 60.669	γ = 120

Symmetry
Space Group	P 61

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	PIXEL	DECTRIS EIGER X 4M		2018-02-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-1A	1.1000	Photon Factory	BL-1A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (All)	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	1.8	47.92	100	0.035	18.2	21.2		68935			17.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.84			0.268	3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation 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)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7D6R	1.8	47.92	1.35	68893	3338	99.98	0.1677	0.1665	0.1665	0.1908	0.1913	18.64

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	6.3168
f_angle_d	0.8634
f_chiral_restr	0.057
f_plane_restr	0.0082
f_bond_d	0.0065

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4955
Nucleic Acid Atoms
Solvent Atoms	490
Heterogen Atoms	53

Software

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