☰ Navigation Tabs
Crystal structure of a protein with alpha-lytic protease prodomain-like fold (BDI_0842) from Parabacteroides distasonis ATCC 8503 at 1.40 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 8.0% ethylene glycol, 20.0% polyethylene glycol 10000, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.3 46.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.405 α = 90 b = 45.673 β = 90 c = 48.105 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 PIXEL DECTRIS PILATUS 6M Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) 2013-02-21 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97917,0.88557,0.97849 SSRL BL11-1
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 1.4 29.529 97.3 0.045 11.89 16677 -3 13.784
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 1.4 1.45 97.7 0.513 1.9
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.4 29.529 16642 845 99.15 0.1309 0.1289 0.1324 0.1679 0.1675 RANDOM 18.916
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] 0.59 -0.55 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.919 r_dihedral_angle_4_deg 20.339 r_dihedral_angle_3_deg 10.302 r_scangle_it 6.728 r_sphericity_free 6.497 r_dihedral_angle_1_deg 5.056 r_scbond_it 4.591 r_mcangle_it 3.512 r_sphericity_bonded 3.202 r_mcbond_it 2.359
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.919 r_dihedral_angle_4_deg 20.339 r_dihedral_angle_3_deg 10.302 r_scangle_it 6.728 r_sphericity_free 6.497 r_dihedral_angle_1_deg 5.056 r_scbond_it 4.591 r_mcangle_it 3.512 r_sphericity_bonded 3.202 r_mcbond_it 2.359 r_rigid_bond_restr 1.761 r_angle_refined_deg 1.416 r_mcbond_other 1.222 r_angle_other_deg 0.92 r_chiral_restr 0.084 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 622 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 8
Software Software Software Name Purpose MolProbity model building PDB_EXTRACT data extraction SHELX phasing SHARP phasing XSCALE data scaling REFMAC refinement XDS data reduction SHELXD phasing