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Crystal structure of P8 from Lactobacillus rhamnosus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 290 0.05M Zinc Acetate dihydrate, 20% PEG3350, 5% n-dodecyl-N, N-dimethylamine-N-oxide
Crystal Properties Matthews coefficient Solvent content 2.43 49.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.86 α = 90 b = 40.86 β = 90 c = 107.01 γ = 90
Symmetry Space Group P 43 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 PIXEL DECTRIS EIGER X 4M 2016-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 0.9738 Photon Factory BL-1A
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 1.56 38.17 99.7 0.111 4.95 20 12894
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.56 1.601 98.98 0.6 0.18
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.56 38.17 12894 697 99.71 0.17862 0.17762 0.19622 0.208 RANDOM 16.651
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] -0.63 -0.63 1.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.153 r_dihedral_angle_4_deg 24.23 r_dihedral_angle_3_deg 10.293 r_dihedral_angle_1_deg 4.709 r_long_range_B_refined 4.6 r_long_range_B_other 4.536 r_scangle_other 3.718 r_scbond_it 2.628 r_scbond_other 2.624 r_mcangle_other 2.392
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.153 r_dihedral_angle_4_deg 24.23 r_dihedral_angle_3_deg 10.293 r_dihedral_angle_1_deg 4.709 r_long_range_B_refined 4.6 r_long_range_B_other 4.536 r_scangle_other 3.718 r_scbond_it 2.628 r_scbond_other 2.624 r_mcangle_other 2.392 r_mcangle_it 2.388 r_angle_refined_deg 1.781 r_mcbond_it 1.648 r_mcbond_other 1.6 r_angle_other_deg 1.586 r_chiral_restr 0.084 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 607 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling AutoSol phasing