9IJ6 | pdb_00009ij6

Crystal structure of the complex of erythrose-4-phosphate dehydrogenase from Acinetobacter baumannii with Adenosine phosphate at 2.40 A resolution.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8ZN4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION7.52980.2M MgSO4.6H2O, 0.1M HEPES sodium (pH 7.5)
Crystal Properties
Matthews coefficientSolvent content
3.1460.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 147.578α = 90
b = 167.012β = 90
c = 155.058γ = 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
12.483.6461000.2140.2270.0710.9967.69.174905
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)
12.42.451002.052.170.70.619.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.483.64674868111199.9440.170.16960.180.21960.2350.406
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]
-0.61-4.7435.353
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.672
r_dihedral_angle_6_deg14.334
r_lrange_it10.192
r_lrange_other10.189
r_scangle_other8.251
r_scangle_it8.25
r_dihedral_angle_2_deg7.636
r_dihedral_angle_1_deg7.15
r_mcangle_it5.889
r_mcangle_other5.889
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.672
r_dihedral_angle_6_deg14.334
r_lrange_it10.192
r_lrange_other10.189
r_scangle_other8.251
r_scangle_it8.25
r_dihedral_angle_2_deg7.636
r_dihedral_angle_1_deg7.15
r_mcangle_it5.889
r_mcangle_other5.889
r_scbond_it5.213
r_scbond_other5.213
r_mcbond_it3.962
r_mcbond_other3.954
r_angle_refined_deg1.527
r_angle_other_deg0.509
r_symmetry_nbd_other0.211
r_nbd_refined0.204
r_nbtor_refined0.177
r_nbd_other0.177
r_dihedral_angle_other_2_deg0.17
r_xyhbond_nbd_refined0.168
r_symmetry_nbd_refined0.132
r_symmetry_xyhbond_nbd_other0.117
r_symmetry_xyhbond_nbd_refined0.089
r_symmetry_nbtor_other0.083
r_chiral_restr0.067
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10717
Nucleic Acid Atoms
Solvent Atoms692
Heterogen Atoms122

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building