1R1Z

The Crystal structure of the Carbohydrate recognition domain of the glycoprotein sorting receptor p58/ERGIC-53 reveals a novel metal binding site and conformational changes associated with calcium ion binding

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	PEG8000, Calcium Chloride, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.351	α = 91.05
b = 81.068	β = 94.14
c = 82.306	γ = 94.99

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 4		2002-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.934	ESRF	ID14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.4	10	95.7	0.126	0.096	13	2.3	98470	42617	1	1	45.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.4	2.53	95.7		0.43	0.33	1.7	2.3	6205

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1gv9	2.4	10	0.005	0.005	42617	41040	1071	94.55	0.223	0.22297	0.2225	0.24063	RANDOM	21.012

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]
1.56	-2.51	-1.35	-3.33	0.89	1.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.256
r_scangle_it	2.33
r_scbond_it	1.457
r_angle_refined_deg	1.225
r_mcangle_it	0.944
r_mcbond_it	0.496
r_symmetry_vdw_refined	0.425
r_symmetry_hbond_refined	0.313
r_nbd_refined	0.223
r_xyhbond_nbd_refined	0.204

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.256
r_scangle_it	2.33
r_scbond_it	1.457
r_angle_refined_deg	1.225
r_mcangle_it	0.944
r_mcbond_it	0.496
r_symmetry_vdw_refined	0.425
r_symmetry_hbond_refined	0.313
r_nbd_refined	0.223
r_xyhbond_nbd_refined	0.204
r_chiral_restr	0.089
r_bond_refined_d	0.012
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7592
Nucleic Acid Atoms
Solvent Atoms	193
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
AMoRE	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.