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Crystal structure of vWFA domain from LapA adhesin of Pseudomonas fluorescens
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 5.5 295 PEG 8000, cacodylate, calcium acetate
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.253 α = 90 b = 84.226 β = 90 c = 96.233 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 RIGAKU RAXIS IV 2020-03-05 M SINGLE WAVELENGTH 2 1 x-ray 100 PIXEL DECTRIS EIGER X 9M 2020-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 2.29 2 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.98400 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2 1.45 48.12 100 0.078 0.081 0.022 0.999 20.1 13.1 105997 13.036
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 1.45 1.47 100 0.941 0.306 0.867 2.6 11.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD FREE R-VALUE 1.45 48.163 105912 5261 99.993 0.171 0.1701 0.1712 0.1857 0.1868 5% 18.787
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] 1.332 -0.353 -0.979
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.894 r_dihedral_angle_3_deg 11.066 r_dihedral_angle_2_deg 6.53 r_dihedral_angle_1_deg 6.178 r_lrange_it 5.205 r_scangle_it 3.2 r_scbond_it 2.238 r_mcangle_it 2.046 r_angle_refined_deg 1.459 r_mcbond_it 1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.894 r_dihedral_angle_3_deg 11.066 r_dihedral_angle_2_deg 6.53 r_dihedral_angle_1_deg 6.178 r_lrange_it 5.205 r_scangle_it 3.2 r_scbond_it 2.238 r_mcangle_it 2.046 r_angle_refined_deg 1.459 r_mcbond_it 1.33 r_nbtor_refined 0.309 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.154 r_symmetry_xyhbond_nbd_refined 0.145 r_symmetry_nbd_refined 0.134 r_ncsr_local_group_3 0.096 r_chiral_restr 0.09 r_ncsr_local_group_2 0.087 r_ncsr_local_group_1 0.075 r_metal_ion_refined 0.073 r_gen_planes_refined 0.007 r_bond_refined_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4191 Nucleic Acid Atoms Solvent Atoms 725 Heterogen Atoms 20
Software Software Software Name Purpose XDS data reduction Aimless data scaling AutoSol phasing REFMAC refinement