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Structure of active wild-type Prevotella intermedia interpain A cysteine protease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BB7 PDB ENTRY 3BB7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 28% PEG 4000, 0.2M magnesium chloride, 30% xylitol, 0.1M Tris HCl, pH8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.13 60.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.241 α = 90 b = 129.241 β = 90 c = 81.97 γ = 90
Symmetry Space Group P 41 21 2
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 ADSC QUANTUM 315 2006-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9760 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3.2 47.25 99 0.329 6.2 7.9 13017 13017 1.5 46.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.4 98.2 0.897 1.9 7.9
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 PDB ENTRY 3BB7 3.2 47.25 11333 11333 570 99.72 0.20977 0.20977 0.20725 0.2144 0.26117 0.2722 RANDOM 56.898
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] 3.01 3.01 -6.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.599 r_dihedral_angle_3_deg 17.952 r_dihedral_angle_4_deg 13.252 r_dihedral_angle_1_deg 6.34 r_angle_refined_deg 1.31 r_scangle_it 0.995 r_angle_other_deg 0.885 r_scbond_it 0.654 r_mcangle_it 0.378 r_mcbond_it 0.277
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.599 r_dihedral_angle_3_deg 17.952 r_dihedral_angle_4_deg 13.252 r_dihedral_angle_1_deg 6.34 r_angle_refined_deg 1.31 r_scangle_it 0.995 r_angle_other_deg 0.885 r_scbond_it 0.654 r_mcangle_it 0.378 r_mcbond_it 0.277 r_nbd_refined 0.222 r_symmetry_vdw_refined 0.201 r_nbtor_refined 0.197 r_nbd_other 0.191 r_symmetry_vdw_other 0.178 r_xyhbond_nbd_refined 0.162 r_nbtor_other 0.089 r_chiral_restr 0.069 r_mcbond_other 0.058 r_xyhbond_nbd_other 0.041 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3797 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing