3IVE

Putative 5'-Nucleotidase (c4898) from Escherichia Coli in complex with Cytidine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IVDPDB entry 3IVD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.529825% PEG 3350, 0.2M LiSo4, 0.1M Bis-Tris pH 5.5, Vapor diffusion, Sitting drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4850.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 156.261α = 90
b = 77.453β = 103.83
c = 47.518γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-03-25SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A0.9793NSLSX29A

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
11.75095.80.1027.43.857862
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)
1.71.7677.10.4423.54653

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 3IVD1.75057858292395.740.1670.1650.19RANDOM16.806
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]
-0.57-0.151.4-0.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.015
r_dihedral_angle_4_deg15.856
r_dihedral_angle_3_deg12.68
r_dihedral_angle_1_deg5.872
r_scangle_it4.04
r_scbond_it2.432
r_mcangle_it1.373
r_angle_refined_deg1.324
r_mcbond_it0.726
r_chiral_restr0.093
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.015
r_dihedral_angle_4_deg15.856
r_dihedral_angle_3_deg12.68
r_dihedral_angle_1_deg5.872
r_scangle_it4.04
r_scbond_it2.432
r_mcangle_it1.373
r_angle_refined_deg1.324
r_mcbond_it0.726
r_chiral_restr0.093
r_bond_refined_d0.013
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3863
Nucleic Acid Atoms
Solvent Atoms357
Heterogen Atoms25

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction
MOLREPphasing