3GFZ

Klebsiella pneumoniae BlrP1 pH 6 manganese/cy-diGMP complex


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.5277protein in 5 mM cy-diGMP, 5 mM CaCl2, 25 mM Tris-HCl pH 8.0, 40 mM NaCl, 5 mM MgCl2, 2 mM EDTA, 2 mM DTE, 5% glycerol, reservoir 0.1 M Na-Ac buffer pH 4.5, 0.2 M Ca-acetate, 17-20%PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3447.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.45α = 90
b = 97.09β = 90
c = 127.17γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDMARMOSAIC 225 mm CCD2007-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.98407SLSX10SA

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
12.0548.5493.20.06613.64.34973949739
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)
12.052.1581.90.3863.63.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2.0548.544973949739261897.140.231050.231050.228950.27151RANDOM38.857
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]
-0.47-33.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.733
r_dihedral_angle_4_deg15.725
r_dihedral_angle_3_deg14.442
r_dihedral_angle_1_deg8.461
r_angle_refined_deg1.596
r_scangle_it1.48
r_scbond_it0.971
r_angle_other_deg0.868
r_mcangle_it0.621
r_mcbond_it0.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.733
r_dihedral_angle_4_deg15.725
r_dihedral_angle_3_deg14.442
r_dihedral_angle_1_deg8.461
r_angle_refined_deg1.596
r_scangle_it1.48
r_scbond_it0.971
r_angle_other_deg0.868
r_mcangle_it0.621
r_mcbond_it0.55
r_symmetry_hbond_refined0.204
r_xyhbond_nbd_refined0.193
r_symmetry_vdw_other0.187
r_nbd_refined0.182
r_nbtor_refined0.176
r_symmetry_vdw_refined0.176
r_xyhbond_nbd_other0.161
r_nbd_other0.153
r_chiral_restr0.136
r_nbtor_other0.085
r_mcbond_other0.079
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6174
Nucleic Acid Atoms
Solvent Atoms346
Heterogen Atoms158

Software

Software
Software NamePurpose
MAR345data collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing