2FT3 | pdb_00002ft3

Crystal structure of the biglycan dimer core protein

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XKU	PDB ENTRY 1XKU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	0.2 M triammonium citrate, 20% (v/v) polyethylene glycol 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.45	64.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 206.511	α = 90
b = 119.222	β = 116.61
c = 140.625	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	90	CCD	ADSC QUANTUM 4		2004-06-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.1159	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.4	22.9	96.5			40497	40497

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.4	3.58	97.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1XKU	3.4	23	42108	40497	2040	96.52	0.259	0.259	0.258	0.291	0.2933	RANDOM	38.068

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]
0.91		2.49	-0.85		2.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.673
r_dihedral_angle_4_deg	22.843
r_dihedral_angle_3_deg	17.929
r_dihedral_angle_1_deg	4.934
r_angle_refined_deg	2.276
r_symmetry_vdw_refined	0.375
r_nbtor_refined	0.36
r_nbd_refined	0.313
r_xyhbond_nbd_refined	0.227
r_chiral_restr	0.127
r_symmetry_hbond_refined	0.094
r_bond_refined_d	0.023
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14512
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	162

Software

Software
Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling