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Crystal structure of Hemolysin co-regulated protein 1 (Hcp1) VariantB from Burkholderia pseudomallei
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 291 1.5 M ammonium sulfate, 3.75% v/v 2-propanol, 25% glycerol
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.721 α = 90 b = 82.721 β = 90 c = 64.066 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX300-HS 2021-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 0.999840 NSRRC TPS 05A
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 1 1.58 47.76 95.9 0.044 0.048 0.021 1 22.8 9.8 32755 29.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.58 1.61 71.3 2.013 2.503 1.458 0.258 0.7 4.4
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.582 47.76 32753 1558 95.926 0.226 0.2247 0.2243 0.243 0.2426 35.751
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] -1.131 -0.566 -1.131 3.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.141 r_dihedral_angle_3_deg 11.941 r_lrange_it 9.886 r_lrange_other 9.883 r_scangle_it 6.841 r_scangle_other 6.83 r_dihedral_angle_1_deg 6.656 r_mcangle_it 5.117 r_mcangle_other 5.115 r_scbond_it 4.542
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.141 r_dihedral_angle_3_deg 11.941 r_lrange_it 9.886 r_lrange_other 9.883 r_scangle_it 6.841 r_scangle_other 6.83 r_dihedral_angle_1_deg 6.656 r_mcangle_it 5.117 r_mcangle_other 5.115 r_scbond_it 4.542 r_scbond_other 4.518 r_dihedral_angle_2_deg 4.286 r_mcbond_it 3.556 r_mcbond_other 3.554 r_angle_refined_deg 1.664 r_angle_other_deg 0.575 r_chiral_restr 0.087 r_gen_planes_other 0.017 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2182 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 20
Software Software Software Name Purpose XDS data scaling XDS data reduction Aimless data scaling MOLREP phasing REFMAC refinement