3HY9 | pdb_00003hy9

Crystal Structure of the Catalytic Domain of ADAMTS-5 in Complex with an Amino-2-indanol compound

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3B8Z	PDB ENTRY 3B8Z

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	25% PEG 3350, 200 mM ammonium acetate, 100 mM Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
1.83	32.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.692	α = 90
b = 44.444	β = 90.19
c = 76.458	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	MAR CCD 165 mm		2007-04-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.0	APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.02	50	99.8	0.044	0.044	29.1	3.6	23498	23451	-1.5	-3	19.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.02	2.09	98.2		0.098	0.098	7.8	2.1	2238

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	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 3B8Z	2.02	31.02	22235	1205	99.74	0.16321	0.15912	0.16	0.23793	0.24	RANDOM	20.495

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]
1.62		0.16	-1.33		-0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.693
r_dihedral_angle_4_deg	19.154
r_dihedral_angle_3_deg	15.648
r_dihedral_angle_1_deg	5.865
r_scangle_it	2.939
r_scbond_it	1.882
r_angle_refined_deg	1.354
r_mcangle_it	1.349
r_mcbond_it	0.772
r_nbtor_refined	0.298

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.693
r_dihedral_angle_4_deg	19.154
r_dihedral_angle_3_deg	15.648
r_dihedral_angle_1_deg	5.865
r_scangle_it	2.939
r_scbond_it	1.882
r_angle_refined_deg	1.354
r_mcangle_it	1.349
r_mcbond_it	0.772
r_nbtor_refined	0.298
r_symmetry_vdw_refined	0.212
r_nbd_refined	0.207
r_symmetry_hbond_refined	0.189
r_xyhbond_nbd_refined	0.158
r_metal_ion_refined	0.105
r_chiral_restr	0.087
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3350
Nucleic Acid Atoms
Solvent Atoms	487
Heterogen Atoms	72

Software

Software
Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.