2JC4

3'-5' exonuclease (NExo) from Neisseria Meningitidis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BIXPDB ENTRY 1BIX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5PROTEIN CONCENTRATION 8.7MG/ML BUFFER: 10 MM TRIS, PH 7.0, 100 MM NACL . WELL SOLUTION: 100 MM NA CACODYLATE PH 6 200 MM NA ACETATE, 15 % PEG 8000. THE CRYSTALLISATION PLATES USED WERE CORNING ROUND BOTTOM 96 WELL PLATES. THE CRYSTALLISATION DROPS CONSISTED OF 1UL PROTEIN AND 1UL WELL SOLUTION.
Crystal Properties
Matthews coefficientSolvent content
2.0631.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.193α = 90
b = 58.618β = 90
c = 88.635γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.1SRSPX14.1

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
11.92097.60.0924.56.819164-3
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)
11.91.9791.40.325.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1BIX1.919.96191129821000.1520.150.2020.2RAMDOM16.05
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]
0.1930.079-0.272
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.938
r_dihedral_angle_4_deg17.177
r_dihedral_angle_3_deg12.594
r_dihedral_angle_1_deg6.176
r_scangle_it3.5
r_scbond_it2.328
r_angle_refined_deg1.501
r_mcangle_it1.372
r_mcbond_it0.783
r_nbtor_refined0.308
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2028
Nucleic Acid Atoms
Solvent Atoms287
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing