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XhpG hydrolase mutant S98A of Xenorhabdus hominickii
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, HANGING DROP 6.5 293 20% PEG 8K, 200mM Magnesium acetate, 100mM sodium Cacodylate
Crystal Properties Matthews coefficient Solvent content 2.13 42.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.83 α = 90 b = 68.54 β = 98.11 c = 75.48 γ = 90
Symmetry Space Group C 1 2 1
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 EIGER X 9M 2022-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.82656 SOLEIL PROXIMA 2
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 1.18 39.5 98 0.041 0.044 0.017 0.999 17.9 6.9 78411
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 1.18 1.21 92.7 1.48 1.611 0.625 0.674 6.4
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.18 20 74471 3920 97.87 0.16778 0.1663 0.19625 RANDOM 19.582
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] -0.94 -1.18 -0.89 2.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.716 r_dihedral_angle_2_deg 10.673 r_rigid_bond_restr 9.532 r_dihedral_angle_1_deg 6.271 r_scangle_other 3.735 r_long_range_B_refined 3.495 r_long_range_B_other 3.435 r_scbond_it 3.151 r_scbond_other 3.15 r_mcangle_other 2.338
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.716 r_dihedral_angle_2_deg 10.673 r_rigid_bond_restr 9.532 r_dihedral_angle_1_deg 6.271 r_scangle_other 3.735 r_long_range_B_refined 3.495 r_long_range_B_other 3.435 r_scbond_it 3.151 r_scbond_other 3.15 r_mcangle_other 2.338 r_mcangle_it 2.207 r_mcbond_other 1.848 r_mcbond_it 1.842 r_angle_refined_deg 1.737 r_angle_other_deg 0.584 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 2035 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing