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 |