1JUQ | pdb_00001juq

GGA3 VHS domain complexed with C-terminal peptide from cation-dependent Mannose 6-phosphate receptor

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	Sodium/Potassium phosphate, Lithium Sulfate, CAPS, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.64	α = 90
b = 131.35	β = 90
c = 108.14	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	IMAGE PLATE	RIGAKU RAXIS IV	mirrors	2001-06-23	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 4		2001-06-03	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418
2	SYNCHROTRON	NSLS BEAMLINE X9B	0.97900,0.97946,0.96859	NSLS	X9B

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	2.2	100	97.6	0.051	19.5	3.57		43908	2		28.5

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	2.2	2.28	86.7		0.282	3.97	2.8	3823

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD/FOURIER SYNTHESIS	THROUGHOUT	2.2	90.03	42356	4269	94.2	0.221	0.2208	0.254	0.2548	RANDOM	45.9

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]
-5.89			13.22		-7.33

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	18.7
c_scangle_it	3.46
c_scbond_it	2.34
c_mcangle_it	2.31
c_mcbond_it	1.44
c_angle_deg	1.2
c_improper_angle_d	0.79
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5214
Nucleic Acid Atoms
Solvent Atoms	175
Heterogen Atoms

Software

Software
Software Name	Purpose
SOLVE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.