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Room-temperature structure of PBP2a at EuXFEL
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VQQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 293 0.1 M Hepes pH 7, 25% PEG 1500, 0.88 M NaCl, 0.016 M CdCl2
Crystal Properties Matthews coefficient Solvent content 2.78 55.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.7 α = 90 b = 106.6 β = 90 c = 186.8 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 298 PIXEL AGIPD 2024-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER EUROPEAN XFEL BEAMLINE SPB/SFX 0.133 European XFEL SPB/SFX
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 injection
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.4 26 100 0.98 5 635 23286
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 3.4 3.5 0.32
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 3.5 25.39 20145 1032 99.6 0.24804 0.24456 0.2506 0.31578 0.3196 RANDOM 97.09
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] 0.13 0.23 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.211 r_long_range_B_refined 17.651 r_long_range_B_other 17.65 r_mcangle_it 11.71 r_mcangle_other 11.71 r_scangle_other 9.75 r_dihedral_angle_1_deg 7.11 r_mcbond_it 7.09 r_mcbond_other 7.087 r_scbond_it 6.048
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.211 r_long_range_B_refined 17.651 r_long_range_B_other 17.65 r_mcangle_it 11.71 r_mcangle_other 11.71 r_scangle_other 9.75 r_dihedral_angle_1_deg 7.11 r_mcbond_it 7.09 r_mcbond_other 7.087 r_scbond_it 6.048 r_scbond_other 5.761 r_dihedral_angle_2_deg 3.875 r_angle_refined_deg 1.289 r_angle_other_deg 0.471 r_chiral_restr 0.059 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10291 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction Aimless data scaling PHASER phasing