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Crystal structure of ADAMTS5 with inhibitor bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RJP PDB entry 2RJP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 10% PEG 8000, 0.2 M Ammonium sulfate, 0.1M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.95 58.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.471 α = 90 b = 95.471 β = 90 c = 93.487 γ = 120
Symmetry Space Group P 31 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 MARMOSAIC 300 mm CCD 2006-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.00000 APS 22-ID
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 2.6 50 13624
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 2.6 2.69 0.29 2.5
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2RJP 2.6 50 13609 683 87.52 0.231 0.23 0.26 RANDOM 62.82
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] 3.85 1.93 3.85 -5.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.603 r_dihedral_angle_4_deg 15.061 r_dihedral_angle_3_deg 14.736 r_dihedral_angle_1_deg 4.802 r_scangle_it 1.038 r_angle_refined_deg 0.899 r_scbond_it 0.549 r_mcangle_it 0.38 r_nbtor_refined 0.29 r_mcbond_it 0.198
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.603 r_dihedral_angle_4_deg 15.061 r_dihedral_angle_3_deg 14.736 r_dihedral_angle_1_deg 4.802 r_scangle_it 1.038 r_angle_refined_deg 0.899 r_scbond_it 0.549 r_mcangle_it 0.38 r_nbtor_refined 0.29 r_mcbond_it 0.198 r_nbd_refined 0.167 r_symmetry_vdw_refined 0.15 r_symmetry_hbond_refined 0.13 r_xyhbond_nbd_refined 0.129 r_metal_ion_refined 0.116 r_chiral_restr 0.056 r_symmetry_metal_ion_refined 0.039 r_bond_refined_d 0.006 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2236 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 66
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction