3FBY

The crystal structure of the signature domain of cartilage oligomeric matrix protein.

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1UX6	PDB ENTRY 1UX6 AND 1YO8
experimental model	PDB	1YO8	PDB ENTRY 1UX6 AND 1YO8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	50mM Ammonium Sulfate, 0.05M Bis-Tris, 30% (v/v) Pentaerythritol ethoxylate (15/4 EO/OH), pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
4.23	70.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 192.242	α = 90
b = 192.242	β = 90
c = 145.681	γ = 120

Symmetry
Space Group	P 32 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	100	CCD	ADSC QUANTUM 315	mirror	2008-02-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97945	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	3.15	39	99.9	0.133	15.4	6	53862	53862

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.15	3.26	100		0.88	2.3	6	5338

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1UX6 AND 1YO8	3.15	39	51068	51068	2735	99.73	0.2054	0.2054	0.2023	0.2663	RANDOM	55.482

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]
0.16	0.08		0.16		-0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.991
r_dihedral_angle_3_deg	20.007
r_dihedral_angle_4_deg	19.045
r_dihedral_angle_1_deg	7.246
r_scangle_it	2.949
r_scbond_it	1.709
r_angle_refined_deg	1.632
r_mcangle_it	1.047
r_mcbond_it	0.493
r_chiral_restr	0.119
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12483
Nucleic Acid Atoms
Solvent Atoms	6
Heterogen Atoms	288

Software

Software
Software Name	Purpose
SBC-Collect	data collection
MOLREP	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling