3LJT

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)
TypeSourceAccession CodeDetails
experimental modelPDB 3B8Z 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529825% PEG 3350, 200 mM ammonium acetate, 100 mM Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
1.8132.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.398α = 90
b = 44.518β = 90
c = 76.251γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATEMAR scanner 300 mm plate2008-07-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G1.0APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.650960.07317.65.22095420120-1.5-311.94
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.61.6665.80.3562.22.81542

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT3B8Z1.638.1219840107088.060.161370.159410.19838RANDOM10.354
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]
0.62-0.70.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.705
r_dihedral_angle_4_deg17.564
r_dihedral_angle_3_deg13.844
r_dihedral_angle_1_deg5.83
r_scangle_it3.082
r_scbond_it1.962
r_mcangle_it1.526
r_angle_refined_deg1.442
r_angle_other_deg0.967
r_mcbond_it0.937
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.705
r_dihedral_angle_4_deg17.564
r_dihedral_angle_3_deg13.844
r_dihedral_angle_1_deg5.83
r_scangle_it3.082
r_scbond_it1.962
r_mcangle_it1.526
r_angle_refined_deg1.442
r_angle_other_deg0.967
r_mcbond_it0.937
r_symmetry_vdw_other0.257
r_nbd_refined0.221
r_mcbond_other0.213
r_nbd_other0.203
r_symmetry_vdw_refined0.19
r_symmetry_hbond_refined0.183
r_nbtor_refined0.18
r_xyhbond_nbd_refined0.153
r_nbtor_other0.084
r_chiral_restr0.082
r_metal_ion_refined0.081
r_xyhbond_nbd_other0.068
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1687
Nucleic Acid Atoms
Solvent Atoms293
Heterogen Atoms43

Software

Software
Software NamePurpose
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling