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Crystal structure of shaft pilin spaA from Lactobacillus rhamnosus GG - E139A mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5F44
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 0.1M sodium thiocynate, 15% PEG3350
Crystal Properties Matthews coefficient Solvent content 4.03 69.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 223.95 α = 90 b = 63.488 β = 94.99 c = 104.453 γ = 90
Symmetry Space Group C 1 2 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 2015-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.95372 ESRF BM14
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 2.47 111.8 83.53 0.08946 0.09943 17.36 5 44441
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 2.466 2.554 27.02 0.347 3.84 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 5F44 2.47 111.8 42201 2240 83.46 0.2013 0.20045 0.2073 0.2168 0.226 RANDOM 24.418
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] 1.07 0.56 -3.21 2.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.889 r_dihedral_angle_3_deg 13.48 r_dihedral_angle_4_deg 11.632 r_long_range_B_refined 8.217 r_long_range_B_other 8.217 r_scangle_other 7.396 r_scbond_it 6.699 r_scbond_other 6.699 r_dihedral_angle_1_deg 5.74 r_mcangle_other 3.491
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.889 r_dihedral_angle_3_deg 13.48 r_dihedral_angle_4_deg 11.632 r_long_range_B_refined 8.217 r_long_range_B_other 8.217 r_scangle_other 7.396 r_scbond_it 6.699 r_scbond_other 6.699 r_dihedral_angle_1_deg 5.74 r_mcangle_other 3.491 r_mcangle_it 3.489 r_mcbond_it 3.245 r_mcbond_other 3.211 r_angle_refined_deg 1.1 r_angle_other_deg 0.853 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.003 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6049 Nucleic Acid Atoms Solvent Atoms 286 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing MOLREP phasing Coot model building