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ReoM- Listeria monocytogenes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5US5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 293 0.1 M phosphate/citrate
0.2 lithium sulphate
20 % w/v PEG 1000
Crystal Properties Matthews coefficient Solvent content 2.12 41.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.788 α = 90 b = 58.619 β = 90 c = 74.449 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 EIGER2 XE 16M 2018-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976250 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.6 74.45 99.8 0.986 8.2 4.8 23059
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 0.62 2.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5US5 1.6 37.252 23008 960 99.731 0.156 0.153 0.1532 0.2137 0.1958 25.171
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] 1.516 -2.119 0.603
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.887 r_dihedral_angle_4_deg 18.785 r_dihedral_angle_3_deg 13.152 r_scangle_it 6.224 r_lrange_it 6.152 r_lrange_other 6.117 r_scangle_other 5.699 r_dihedral_angle_1_deg 5.631 r_mcangle_it 5.082 r_mcangle_other 5.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.887 r_dihedral_angle_4_deg 18.785 r_dihedral_angle_3_deg 13.152 r_scangle_it 6.224 r_lrange_it 6.152 r_lrange_other 6.117 r_scangle_other 5.699 r_dihedral_angle_1_deg 5.631 r_mcangle_it 5.082 r_mcangle_other 5.082 r_scbond_it 5.018 r_scbond_other 4.742 r_mcbond_it 4.386 r_mcbond_other 4.372 r_rigid_bond_restr 3.609 r_angle_refined_deg 1.6 r_angle_other_deg 1.458 r_nbd_other 0.236 r_nbd_refined 0.227 r_symmetry_nbd_refined 0.207 r_symmetry_nbd_other 0.202 r_xyhbond_nbd_refined 0.178 r_nbtor_refined 0.174 r_symmetry_xyhbond_nbd_refined 0.169 r_chiral_restr 0.082 r_symmetry_nbtor_other 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_symmetry_xyhbond_nbd_other 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1394 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing