Experiment: 2I2B

 2I2B

Crystal structure of LmNADK1 from Listeria monocytogenes


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2I2APDB ENTRY 2I2A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.40.3 M potassium chloride, 50 mM tri-sodium citrate dihydrate, 15-20% w/v polyethylene glycol 400, pH 5.4, VAPOR DIFFUSION, HANGING DROP, pH 5.40
Crystal Properties
Matthews coefficientSolvent content
2.3347.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.243α = 90
b = 74.565β = 90
c = 118.29γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152005-06-22MSINGLE 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
12.130.9999.90.08218.15.51587828.6
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)
12.12.211000.4882.95.7

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2I2A2.130.99167091587883199.90.2040.2030.231RANDOM22.04
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]
1.152.09-3.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.729
r_dihedral_angle_3_deg16.278
r_dihedral_angle_4_deg13.619
r_dihedral_angle_1_deg9.63
r_angle_refined_deg1.342
r_scangle_it1.296
r_scbond_it0.98
r_mcangle_it0.731
r_xyhbond_nbd_refined0.525
r_mcbond_it0.461
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1995
Nucleic Acid Atoms
Solvent Atoms66
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing