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Crystal structure of a variable region segment of Leptospira host-interacting outer surface protein, LigA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2MOG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 23% PEG 3350, 260mM Potassium Iodide and 100mM Bis-Tris Propane
Crystal Properties Matthews coefficient Solvent content 2.45 49.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.219 α = 90 b = 63.905 β = 90 c = 171.839 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 IMAGE PLATE MAR scanner 345 mm plate 2019-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.87 85.92 98.8 0.113 0.994 9.1 6.7 31943
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 1.87 1.91 0.759
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 2MOG 1.87 85.92 30215 1527 98.35 0.20885 0.20757 0.2114 0.23411 0.2399 RANDOM 21.308
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] -1.41 0.62 0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.367 r_dihedral_angle_3_deg 13.311 r_dihedral_angle_4_deg 7.236 r_long_range_B_refined 6.19 r_dihedral_angle_1_deg 6.082 r_long_range_B_other 6.069 r_scangle_other 3.688 r_scbond_it 2.639 r_scbond_other 2.577 r_mcangle_other 2.032
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.367 r_dihedral_angle_3_deg 13.311 r_dihedral_angle_4_deg 7.236 r_long_range_B_refined 6.19 r_dihedral_angle_1_deg 6.082 r_long_range_B_other 6.069 r_scangle_other 3.688 r_scbond_it 2.639 r_scbond_other 2.577 r_mcangle_other 2.032 r_mcangle_it 2.031 r_mcbond_it 1.41 r_mcbond_other 1.41 r_angle_refined_deg 1.337 r_angle_other_deg 1.02 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2645 Nucleic Acid Atoms Solvent Atoms 315 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement DIALS data reduction pointless data scaling BUCCANEER phasing