4YF1

1.85 angstrom crystal structure of lmo0812 from Listeria monocytogenes EGD-e


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M tri-sodium citrate, pH 5.5, 20% (w/v) PEG 3000
Crystal Properties
Matthews coefficientSolvent content
2.5551.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.811α = 90
b = 58.675β = 114.31
c = 95.73γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2014-10-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

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
11.853099.20.08531.66.575985
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)
11.851.8892.90.6432.365.83546

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 DIFFRACTIONSADTHROUGHOUT1.8529.3471643373599.050.181640.180280.20801RANDOM34.102
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]
4.40.08-2.83-1.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.526
r_dihedral_angle_4_deg16.835
r_dihedral_angle_3_deg11.371
r_long_range_B_refined6.836
r_long_range_B_other6.498
r_scangle_other2.961
r_dihedral_angle_1_deg2.606
r_mcangle_it2.185
r_mcangle_other2.185
r_scbond_it1.779
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.526
r_dihedral_angle_4_deg16.835
r_dihedral_angle_3_deg11.371
r_long_range_B_refined6.836
r_long_range_B_other6.498
r_scangle_other2.961
r_dihedral_angle_1_deg2.606
r_mcangle_it2.185
r_mcangle_other2.185
r_scbond_it1.779
r_scbond_other1.776
r_angle_refined_deg1.38
r_mcbond_it1.336
r_mcbond_other1.336
r_angle_other_deg0.883
r_chiral_restr0.088
r_gen_planes_refined0.023
r_gen_planes_other0.018
r_bond_refined_d0.011
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4997
Nucleic Acid Atoms
Solvent Atoms508
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing