4AVF

Crystal structure of Pseudomonas aeruginosa inosine 5'-monophosphate dehydrogenase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VRDPDB ENTRY 1VRD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.511% PEG 4000, 0.1M MES PH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.1442.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.59α = 90
b = 116.59β = 90
c = 259.17γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRRORS2010-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.231061000.0818.59.1877342
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.232.291000.753.29.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1VRD2.23106.3383337439799.940.180450.179420.20003RANDOM52.371
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]
-0.42-0.420.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.414
r_dihedral_angle_4_deg14.574
r_dihedral_angle_3_deg12.34
r_dihedral_angle_1_deg5.617
r_angle_refined_deg1.242
r_angle_other_deg1.081
r_chiral_restr0.066
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.414
r_dihedral_angle_4_deg14.574
r_dihedral_angle_3_deg12.34
r_dihedral_angle_1_deg5.617
r_angle_refined_deg1.242
r_angle_other_deg1.081
r_chiral_restr0.066
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.004
r_gen_planes_other0.003
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9094
Nucleic Acid Atoms
Solvent Atoms360
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing