6ZQY | pdb_00006zqy

Crystal structure of tetrameric fibrinogen-like recognition domain of FIBCD1 with Neu5Ac ligand bound

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	1.6 M Ammonium Sulphate, 9% Dioxane, 0.1 M MES pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.29	α = 90
b = 119.29	β = 90
c = 44.21	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		2009-04-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.970	Diamond	I04

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	1.85	59.72	98.6	0.076	0.089	0.046	0.993	11.7	3.5		52803

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	1.85	1.89	98.7		0.388	0.469	0.258	0.795		3

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4M7H	1.85	59.72	50114	2688	98.41	0.1761	0.175	0.1849	0.1962	0.2055	RANDOM	16.788

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]
0.5			0.5		-1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.043
r_dihedral_angle_4_deg	15.359
r_dihedral_angle_3_deg	11.888
r_dihedral_angle_1_deg	7.301
r_angle_other_deg	1.266
r_angle_refined_deg	1.26
r_chiral_restr	0.059
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3520
Nucleic Acid Atoms
Solvent Atoms	350
Heterogen Atoms	88

Software

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