1ZS3

The crystal structure of the Lactococcus lactis MG1363 DpsB protein


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62982.0M Sodium Formate, 0.1M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.7457.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.977α = 90
b = 128.379β = 90
c = 193.903γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDADSC QUANTUM 4Mirrors2001-05-11MSINGLE WAVELENGTH
21x-ray298CCDADSC QUANTUM 4Mirrors2001-06-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.20.98SRSPX14.2
2SYNCHROTRONSRS BEAMLINE PX14.20.98SRSPX14.2

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
1,22.71597.80.0740.0747.53.2859128591261.6
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)
2.72.8597.40.4070.4071.73.212388

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1qgh2.7157712577125410892.310.20940.209410.206830.25779RANDOM44.165
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]
-0.140.18-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.715
r_scangle_it3.378
r_scbond_it1.906
r_angle_refined_deg1.692
r_mcangle_it1.66
r_angle_other_deg1.59
r_mcbond_it0.882
r_symmetry_vdw_other0.308
r_symmetry_vdw_refined0.299
r_symmetry_hbond_refined0.269
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.715
r_scangle_it3.378
r_scbond_it1.906
r_angle_refined_deg1.692
r_mcangle_it1.66
r_angle_other_deg1.59
r_mcbond_it0.882
r_symmetry_vdw_other0.308
r_symmetry_vdw_refined0.299
r_symmetry_hbond_refined0.269
r_nbd_other0.237
r_nbd_refined0.234
r_xyhbond_nbd_refined0.192
r_chiral_restr0.098
r_nbtor_other0.097
r_gen_planes_other0.05
r_bond_other_d0.043
r_gen_planes_refined0.025
r_bond_refined_d0.022
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms16644
Nucleic Acid Atoms
Solvent Atoms131
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
CCP4phasing