1XKU

Crystal structure of the dimeric protein core of decorin, the archetypal small leucine-rich repeat proteoglycan

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.75	293	PEG 400, TRIS, OCTYL-BETA-D-GLUCOPYRANOSIDE, SODIUM AZIDE, pH 7.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.31	62.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.78	α = 90
b = 124.145	β = 90
c = 129.609	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV		2002-01-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.15	33.2	98.7	0.048	8.7	10.7	24593	24593			32.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.28	93.7		0.367	2.1	8.2	3266

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SIRAS	THROUGHOUT	2.15	33	24591	24591	1253	98.69	0.19093	0.19093	0.18951	0.21747	RANDOM	39.491

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]
1.92			0.19		-2.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.917
r_dihedral_angle_3_deg	15.199
r_dihedral_angle_4_deg	14.684
r_dihedral_angle_1_deg	5.519
r_scangle_it	4.702
r_scbond_it	2.973
r_angle_refined_deg	1.719
r_mcangle_it	1.632
r_mcbond_it	1.049
r_angle_other_deg	0.539
r_nbtor_refined	0.308
r_nbd_other	0.287
r_symmetry_vdw_refined	0.25
r_nbtor_other	0.239
r_nbd_refined	0.214
r_xyhbond_nbd_refined	0.147
r_symmetry_hbond_refined	0.132
r_chiral_restr	0.117
r_mcbond_other	0.032
r_bond_refined_d	0.021
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2371
Nucleic Acid Atoms
Solvent Atoms	164
Heterogen Atoms	50

Software

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