9I9T | pdb_00009i9t

Room-temperature structure of PBP2a at EuXFEL


X-RAY DIFFRACTION

Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VQQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE2930.1 M Hepes pH 7, 25% PEG 1500, 0.88 M NaCl, 0.016 M CdCl2
Crystal Properties
Matthews coefficientSolvent content
2.7855.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.7α = 90
b = 106.6β = 90
c = 186.8γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298PIXELAGIPD2024-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASEREUROPEAN XFEL BEAMLINE SPB/SFX0.133European XFELSPB/SFX

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1injection

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
13.4261000.98563523286
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.43.50.32

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3.525.3920145103299.60.248040.244560.25060.315780.3196RANDOM97.09
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]
0.130.23-0.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.211
r_long_range_B_refined17.651
r_long_range_B_other17.65
r_mcangle_it11.71
r_mcangle_other11.71
r_scangle_other9.75
r_dihedral_angle_1_deg7.11
r_mcbond_it7.09
r_mcbond_other7.087
r_scbond_it6.048
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.211
r_long_range_B_refined17.651
r_long_range_B_other17.65
r_mcangle_it11.71
r_mcangle_other11.71
r_scangle_other9.75
r_dihedral_angle_1_deg7.11
r_mcbond_it7.09
r_mcbond_other7.087
r_scbond_it6.048
r_scbond_other5.761
r_dihedral_angle_2_deg3.875
r_angle_refined_deg1.289
r_angle_other_deg0.471
r_chiral_restr0.059
r_bond_refined_d0.004
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms10291
Nucleic Acid Atoms
Solvent Atoms135
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
Aimlessdata scaling
PHASERphasing