8ZN4

Crystal structure of Poly(ethylene glycol) stabilized erythrose-4-phosphate dehydrogenase from Acinetobacter baumannii at 2.30 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3CMC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION7.5298A reservoir solution containing 0.2 M MgCl2.6H2O, 0.1 M HEPES sodium (pH 7.5), and 30% v/v PEG 400 was prepared.
Crystal Properties
Matthews coefficientSolvent content
359.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 145.775α = 90
b = 167.135β = 90
c = 150.103γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298PIXELDECTRIS EIGER2 X 9M2023-07-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.87313ESRFID30B

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.346.7031000.20.020.060.99811.213.281357
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)RedundancyNumber Unique Reflections (All)
12.32.341001.581.690.470.822.212.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3CMC2.346.70381321240099.9630.1530.15170.20144.028
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]
1.561-3.6142.053
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.571
r_dihedral_angle_3_deg13.205
r_lrange_it9.593
r_lrange_other9.584
r_dihedral_angle_2_deg8.827
r_scangle_it7.528
r_scangle_other7.528
r_dihedral_angle_1_deg7.008
r_mcangle_it5.144
r_mcangle_other5.143
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.571
r_dihedral_angle_3_deg13.205
r_lrange_it9.593
r_lrange_other9.584
r_dihedral_angle_2_deg8.827
r_scangle_it7.528
r_scangle_other7.528
r_dihedral_angle_1_deg7.008
r_mcangle_it5.144
r_mcangle_other5.143
r_scbond_it4.988
r_scbond_other4.988
r_mcbond_it3.591
r_mcbond_other3.59
r_angle_refined_deg1.547
r_angle_other_deg0.52
r_metal_ion_refined0.259
r_dihedral_angle_other_2_deg0.241
r_symmetry_nbd_other0.214
r_nbd_other0.203
r_nbd_refined0.201
r_symmetry_nbd_refined0.184
r_nbtor_refined0.176
r_symmetry_xyhbond_nbd_refined0.171
r_xyhbond_nbd_refined0.162
r_symmetry_nbtor_other0.085
r_chiral_restr0.071
r_symmetry_xyhbond_nbd_other0.023
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d0.005
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10716
Nucleic Acid Atoms
Solvent Atoms641
Heterogen Atoms488

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building