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The staphostatin-staphopain complex: a forward binding inhibitor in complex with its target cysteine protease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CV8 1CV8, 1NYC experimental model PDB 1NYC 1CV8, 1NYC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.3 294 2 M (NH4)2SO4 and 5% isopropanol, 100 mM guanidinium hydrochloride, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.83 56.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.485 α = 90 b = 94.966 β = 90 c = 110.927 γ = 90
Symmetry Space Group P 21 21 21
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 MARRESEARCH 2003-01-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.05 MPG/DESY, HAMBURG BW6
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 1.8 20.92 94.6 0.052 0.052 9.8 72496 66436 35
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) 1.8 1.9 89.3 0.182 0.182 3.5 2.7 3959
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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1CV8, 1NYC 1.8 10 64796 64796 3406 94.64 0.1921 0.1921 0.19055 0.1994 0.22129 0.2291 RANDOM 27.263
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] 0.21 0.36 -0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.644 r_angle_other_deg 3.935 r_scangle_it 3.473 r_mcangle_it 3.032 r_scbond_it 2.272 r_mcbond_it 1.933 r_angle_refined_deg 1.565 r_symmetry_vdw_other 0.371 r_nbd_other 0.31 r_nbd_refined 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.644 r_angle_other_deg 3.935 r_scangle_it 3.473 r_mcangle_it 3.032 r_scbond_it 2.272 r_mcbond_it 1.933 r_angle_refined_deg 1.565 r_symmetry_vdw_other 0.371 r_nbd_other 0.31 r_nbd_refined 0.24 r_symmetry_vdw_refined 0.222 r_symmetry_hbond_refined 0.206 r_xyhbond_nbd_refined 0.18 r_chiral_restr 0.117 r_nbtor_other 0.115 r_bond_refined_d 0.02 r_gen_planes_other 0.011 r_gen_planes_refined 0.008 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4816 Nucleic Acid Atoms Solvent Atoms 458 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing FFFEAR phasing ARP/wARP model building