4QQ3

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP828910% PEG 2000, 19.3% PEG 200, 0.05 M Tris-buffer, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.4549.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.9α = 90
b = 106.9β = 90
c = 65.489γ = 90
Symmetry
Space GroupP 4 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-05-23MSINGLE 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)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
11.7238.698.40.06612.212.1402504025033.7
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)
11.721.7582.50.4992.14.91623

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4QNE1.7238.64020740207199298.430.1680.1680.16670.1931RANDOM35.722
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]
-1.11-1.112.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.039
r_dihedral_angle_4_deg19.981
r_dihedral_angle_3_deg14.969
r_dihedral_angle_1_deg5.808
r_mcangle_it2.866
r_mcbond_it2.01
r_mcbond_other2.008
r_angle_refined_deg1.695
r_angle_other_deg0.837
r_chiral_restr0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.039
r_dihedral_angle_4_deg19.981
r_dihedral_angle_3_deg14.969
r_dihedral_angle_1_deg5.808
r_mcangle_it2.866
r_mcbond_it2.01
r_mcbond_other2.008
r_angle_refined_deg1.695
r_angle_other_deg0.837
r_chiral_restr0.1
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2187
Nucleic Acid Atoms
Solvent Atoms188
Heterogen Atoms26

Software

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