8ZN1

Structure of erythrose-4-phosphate dehydrogenase from Acinetobacter baumannii at 3.00 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
3.160.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 147.646α = 90
b = 167.88β = 90
c = 152.269γ = 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
1349.5361000.730.790.210.9717.313.538162
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)
133.131002.862.980.780.691.914.4

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-VALUE3CMC349.5363811675499.8930.1670.16580.241948.146
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]
-0.227-3.7984.025
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.348
r_dihedral_angle_6_deg13.206
r_lrange_it9.201
r_lrange_other9.2
r_dihedral_angle_2_deg8.761
r_dihedral_angle_1_deg6.871
r_scangle_it6.858
r_scangle_other6.845
r_mcangle_it5.405
r_mcangle_other5.405
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.348
r_dihedral_angle_6_deg13.206
r_lrange_it9.201
r_lrange_other9.2
r_dihedral_angle_2_deg8.761
r_dihedral_angle_1_deg6.871
r_scangle_it6.858
r_scangle_other6.845
r_mcangle_it5.405
r_mcangle_other5.405
r_scbond_it4.209
r_scbond_other4.2
r_mcbond_it3.379
r_mcbond_other3.377
r_angle_refined_deg1.499
r_angle_other_deg0.506
r_dihedral_angle_other_2_deg0.435
r_nbd_other0.349
r_symmetry_nbd_other0.212
r_nbd_refined0.209
r_nbtor_refined0.18
r_symmetry_nbd_refined0.169
r_xyhbond_nbd_refined0.167
r_symmetry_nbtor_other0.083
r_chiral_restr0.065
r_symmetry_xyhbond_nbd_other0.031
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 Atoms10716
Nucleic Acid Atoms
Solvent Atoms265
Heterogen Atoms216

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building