3GNL

Structure of uncharacterized protein (LMOf2365_1472) from Listeria monocytogenes serotype 4b


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52980.1M Sodium Cacodylate pH 6.5, 30% PEG 6K , 0.2M Sodium Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthew coefficientSolvent content
2.2846.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.273α = 90
b = 84.802β = 90
c = 91.168γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-12-05SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A0.979NSLSX29A

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
11.54099.90.0834.28411.381636
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)
1.51.551000.4878.18077

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONTHROUGHOUT1.54081539408899.880.1980.1960.224RANDOM24.724
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]
0.20.06-0.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.014
r_dihedral_angle_4_deg15.806
r_dihedral_angle_3_deg14.027
r_dihedral_angle_1_deg5.538
r_scangle_it3.437
r_mcangle_it2.388
r_scbond_it2.17
r_angle_refined_deg1.641
r_mcbond_it1.484
r_chiral_restr0.117
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.014
r_dihedral_angle_4_deg15.806
r_dihedral_angle_3_deg14.027
r_dihedral_angle_1_deg5.538
r_scangle_it3.437
r_mcangle_it2.388
r_scbond_it2.17
r_angle_refined_deg1.641
r_mcbond_it1.484
r_chiral_restr0.117
r_bond_refined_d0.017
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3741
Nucleic Acid Atoms
Solvent Atoms459
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction
SHELXDphasing
SHELXEmodel building
CCP4phasing