6ZR3

Crystal structure of tetrameric fibrinogen-like recognition domain of FIBCD1 with N-acetyl-galactosamine-4-sulfate ligand bound

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4M7H	pdbid 4M7H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	1.7 M Ammonium Sulphate, 8% Dioxane, 0.1 M MES pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
3.05	59.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.019	α = 90
b = 119.019	β = 90
c = 44.31	γ = 90

Symmetry
Space Group	P 4

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 2M		2013-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.920	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.97	53.28	97.3	0.102	0.118	0.056	0.976	7.5	3.9		42961

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.97	2.02	98.1		0.27	0.322	0.172	0.888		3.1

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdbid 4M7H	1.97	53.28	40849	2070	96.51	0.1862	0.1843	0.2258	RANDOM	23.457

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]
0.8			0.8		-1.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.807
r_dihedral_angle_4_deg	18.183
r_dihedral_angle_3_deg	13.04
r_dihedral_angle_1_deg	7.544
r_angle_refined_deg	1.351
r_angle_other_deg	1.281
r_chiral_restr	0.063
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.807
r_dihedral_angle_4_deg	18.183
r_dihedral_angle_3_deg	13.04
r_dihedral_angle_1_deg	7.544
r_angle_refined_deg	1.351
r_angle_other_deg	1.281
r_chiral_restr	0.063
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3514
Nucleic Acid Atoms
Solvent Atoms	235
Heterogen Atoms	70

Software

Software
Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
REFMAC	phasing

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.