6ZQR

Crystal structure of tetrameric fibrinogen-like recognition domain of FIBCD1 with GlcNAc 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	1.5 M Ammonium Sulphate, 7% Dioxane, 0.1 M MES pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.6	α = 90
b = 113.6	β = 90
c = 44.08	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	CCD	ADSC QUANTUM 315		2011-01-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.9795	Diamond	I02

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	1.93	56.86	98.7	0.073	0.086	0.044	0.997	12.4	3.5		42095

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	1.93	1.98	98.5		0.379	0.453	0.243	0.796		3.2

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	1.93	56.8	40018	2077	98.38	0.1683	0.1671	0.1912	RANDOM	18.312

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]
0.61			0.61		-1.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.237
r_dihedral_angle_4_deg	16.816
r_dihedral_angle_3_deg	12.959
r_dihedral_angle_1_deg	7.373
r_angle_refined_deg	1.409
r_angle_other_deg	1.346
r_chiral_restr	0.073
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.237
r_dihedral_angle_4_deg	16.816
r_dihedral_angle_3_deg	12.959
r_dihedral_angle_1_deg	7.373
r_angle_refined_deg	1.409
r_angle_other_deg	1.346
r_chiral_restr	0.073
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3520
Nucleic Acid Atoms
Solvent Atoms	248
Heterogen Atoms	97

Software

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

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.