4X3Z

Inosine 5'-monophosphate dehydrogenase from Vibrio cholerae, deletion mutant, in complex with XMP and NAD


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4QNE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72891.03 M sodium/phosphate buffer, 0.15 M malate, 3% PEG-300
Crystal Properties
Matthews coefficientSolvent content
2.3347.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.262α = 90
b = 91.262β = 90
c = 171.214γ = 90
Symmetry
Space GroupP 4 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9792APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.62501000.0670.0710.02510.88.2924779247729.6
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)
11.621.651000.7430.7960.2830.8392.847.84551

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 REPLACEMENTTHROUGHOUT4QNE1.6244.287862455299.920.153450.1520.18157RANDOM23.896
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]
0.10.1-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.198
r_dihedral_angle_4_deg18.088
r_dihedral_angle_3_deg12.553
r_dihedral_angle_1_deg6.062
r_long_range_B_refined6.011
r_long_range_B_other5.712
r_scangle_other3.825
r_scbond_it2.491
r_scbond_other2.479
r_mcangle_it2.369
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.198
r_dihedral_angle_4_deg18.088
r_dihedral_angle_3_deg12.553
r_dihedral_angle_1_deg6.062
r_long_range_B_refined6.011
r_long_range_B_other5.712
r_scangle_other3.825
r_scbond_it2.491
r_scbond_other2.479
r_mcangle_it2.369
r_mcangle_other2.369
r_angle_refined_deg1.919
r_mcbond_it1.604
r_mcbond_other1.604
r_angle_other_deg0.863
r_chiral_restr0.1
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms5029
Nucleic Acid Atoms
Solvent Atoms563
Heterogen Atoms149

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
PDB_EXTRACTdata extraction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing