2I8D

Crystal structure of an uncharacterized conserved protein of COG5646 (ZP_00384875.1) from Lactobacillus casei ATCC 334 at 1.69 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP, NANODROP42771.0M LiCl, 20.0% PEG-6000, 0.1M Citrate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, <NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP, NANODROP
Crystal Properties
Matthews coefficientSolvent content
2.55715851.899723

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.946α = 90
b = 69.276β = 90
c = 90.872γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDAdjustable focusing mirrors in K-B geometry2006-08-11MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.94926,0.97925APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.629.77599.90.0810.0814.73.63461223.99
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.691.731000.6620.6621.13.72504

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 DIFFRACTIONMADTHROUGHOUT1.6929.77534565174099.840.1690.1680.197RANDOM21.732
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]
0.860.13-1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.161
r_dihedral_angle_4_deg17.39
r_dihedral_angle_3_deg13.892
r_scangle_it5.27
r_dihedral_angle_1_deg5.251
r_scbond_it3.853
r_mcangle_it2.579
r_mcbond_it2.074
r_angle_refined_deg1.365
r_angle_other_deg0.866
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.161
r_dihedral_angle_4_deg17.39
r_dihedral_angle_3_deg13.892
r_scangle_it5.27
r_dihedral_angle_1_deg5.251
r_scbond_it3.853
r_mcangle_it2.579
r_mcbond_it2.074
r_angle_refined_deg1.365
r_angle_other_deg0.866
r_mcbond_other0.517
r_nbd_refined0.24
r_symmetry_vdw_other0.209
r_symmetry_vdw_refined0.197
r_nbd_other0.188
r_nbtor_refined0.183
r_xyhbond_nbd_refined0.164
r_symmetry_hbond_refined0.132
r_nbtor_other0.085
r_chiral_restr0.082
r_bond_refined_d0.016
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1998
Nucleic Acid Atoms
Solvent Atoms307
Heterogen Atoms31

Software

Software
Software NamePurpose
MolProbitymodel building
SHELXphasing
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling
SHELXDphasing
autoSHARPphasing