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Crystal structure of Anaplasma phagocytophilum p44-23 outer membrane protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 294 0.2 M ammonium acetate
0.1 M Tris (8.0)
20% PEG 500
Crystal Properties Matthews coefficient Solvent content 1.96 37.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.63 α = 84.42 b = 43.26 β = 69.41 c = 47.8 γ = 89.99
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 2023-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.7054 Diamond I03
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 1.65 44.5 94 0.051 0.999 12.7 3.7 28346
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.74 95.4 0.317 0.938 3.1
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.65 44.5 27005 1341 93.96 0.20685 0.20435 0.2156 0.25344 0.2643 RANDOM 27.158
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] 0.53 0.42 1.01 4.44 -2.01 -3.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.823 r_dihedral_angle_3_deg 17.234 r_dihedral_angle_4_deg 12.975 r_rigid_bond_restr 12.481 r_long_range_B_refined 8.405 r_long_range_B_other 8.33 r_scangle_other 7.455 r_dihedral_angle_1_deg 7.198 r_mcangle_it 6.833 r_mcangle_other 6.833
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.823 r_dihedral_angle_3_deg 17.234 r_dihedral_angle_4_deg 12.975 r_rigid_bond_restr 12.481 r_long_range_B_refined 8.405 r_long_range_B_other 8.33 r_scangle_other 7.455 r_dihedral_angle_1_deg 7.198 r_mcangle_it 6.833 r_mcangle_other 6.833 r_scbond_it 6.675 r_scbond_other 6.672 r_mcbond_it 5.732 r_mcbond_other 5.715 r_angle_refined_deg 2.05 r_angle_other_deg 1.426 r_chiral_restr 0.097 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_bond_other_d 0.006 r_gen_planes_other 0.002 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2232 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction SCALA data scaling PHASER phasing