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THE 1.21 A CRYSTAL STRUCTURE OF HUMAN CATHEPSIN G IN COMPLEX WITH N-[2-[6-fluoro-2-[(4-hydroxy-5-methyl-2-oxo-5-phenylfuran-3-yl)-phenylmethyl]-1H-indol-3-yl]ethyl]acetamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other apo structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7.5 293 0.2 M LiSO4 (Salt),
25 %w/v PEG3350 (Precipitant),
0.1 M HEPES 7.5 pH (Buffer),
Protein was at 17 mg/mL.
Crystal Properties Matthews coefficient Solvent content 2.15 42.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.11 α = 90 b = 74.45 β = 90.3 c = 60.65 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 100 CCD MARMOSAIC 225 mm CCD 2006-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.9999 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.21 60.63 88.9 0.072 0.078 16.66 117974
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.21 1.28 60 0.378 0.432
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.21 60.63 112057 5916 88.91 0.15797 0.15677 0.18106 0.1949 RANDOM 14.404
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] -0.22 -0.14 -0.73 0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.668 r_dihedral_angle_4_deg 12.831 r_dihedral_angle_3_deg 11.624 r_sphericity_free 6.183 r_dihedral_angle_1_deg 6.146 r_sphericity_bonded 3.181 r_scangle_it 3.071 r_scbond_it 2.428 r_mcangle_it 1.894 r_mcbond_it 1.597
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.668 r_dihedral_angle_4_deg 12.831 r_dihedral_angle_3_deg 11.624 r_sphericity_free 6.183 r_dihedral_angle_1_deg 6.146 r_sphericity_bonded 3.181 r_scangle_it 3.071 r_scbond_it 2.428 r_mcangle_it 1.894 r_mcbond_it 1.597 r_angle_refined_deg 1.538 r_rigid_bond_restr 1.292 r_angle_other_deg 0.829 r_mcbond_other 0.627 r_symmetry_vdw_other 0.284 r_nbd_refined 0.193 r_nbd_other 0.192 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.164 r_symmetry_hbond_refined 0.147 r_symmetry_vdw_refined 0.129 r_metal_ion_refined 0.111 r_chiral_restr 0.096 r_nbtor_other 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3621 Nucleic Acid Atoms Solvent Atoms 440 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction PHASER phasing