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Structure of profragilysin-3 from Bacteroides fragilis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 297 100mM sodium citrate dihydrate, 20% PEG 3000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.56 51.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.74 α = 90 b = 69.14 β = 91.57 c = 158.91 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 ADSC QUANTUM 315r 2009-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.0723 ESRF ID23-1
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 1.8 50 98.9 0.075 164503 164503
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 SAD THROUGHOUT 1.8 50 164503 163722 781 98.89 0.16988 0.16971 0.1767 0.20436 0.208 RANDOM 33.719
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] -0.3 0.05 0.4 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.952 r_dihedral_angle_3_deg 13.341 r_dihedral_angle_4_deg 12.933 r_dihedral_angle_1_deg 6.396 r_scangle_it 3.331 r_scbond_it 2.072 r_mcangle_it 1.463 r_angle_refined_deg 1.271 r_angle_other_deg 0.824 r_mcbond_it 0.792
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.952 r_dihedral_angle_3_deg 13.341 r_dihedral_angle_4_deg 12.933 r_dihedral_angle_1_deg 6.396 r_scangle_it 3.331 r_scbond_it 2.072 r_mcangle_it 1.463 r_angle_refined_deg 1.271 r_angle_other_deg 0.824 r_mcbond_it 0.792 r_mcbond_other 0.181 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_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 11311 Nucleic Acid Atoms Solvent Atoms 1147 Heterogen Atoms 75
Software Software Software Name Purpose ProDC data collection SHELXS phasing REFMAC refinement XDS data reduction SCALA data scaling