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Klebsiella pneumoniae BlrP1 pH 8.0 calcium/cy-diGMP complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 277 protein 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 coefficient Solvent content 2.35 47.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.85 α = 90 b = 96.69 β = 90 c = 127.04 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 CCD MARMOSAIC 225 mm CCD 2007-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.97815 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.3 20 97 0.077 21.8 8 36387 36387
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.4 93.7 0.332 7 7.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 2.3 20 36387 36387 1947 99.99 0.24613 0.24613 0.24356 0.2477 0.29551 0.2972 RANDOM 27.931
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] 0.92 -2.42 1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.801 r_dihedral_angle_3_deg 14.447 r_dihedral_angle_4_deg 14.298 r_dihedral_angle_1_deg 7.117 r_angle_refined_deg 1.353 r_scangle_it 0.863 r_angle_other_deg 0.723 r_mcangle_it 0.531 r_scbond_it 0.5 r_mcbond_it 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.801 r_dihedral_angle_3_deg 14.447 r_dihedral_angle_4_deg 14.298 r_dihedral_angle_1_deg 7.117 r_angle_refined_deg 1.353 r_scangle_it 0.863 r_angle_other_deg 0.723 r_mcangle_it 0.531 r_scbond_it 0.5 r_mcbond_it 0.304 r_symmetry_vdw_refined 0.224 r_symmetry_vdw_other 0.203 r_nbd_refined 0.182 r_nbtor_refined 0.171 r_nbd_other 0.162 r_metal_ion_refined 0.149 r_symmetry_hbond_refined 0.136 r_xyhbond_nbd_refined 0.125 r_nbtor_other 0.079 r_chiral_restr 0.06 r_mcbond_other 0.041 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other 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 Atoms Number Protein Atoms 6163 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 158
Software Software Software Name Purpose MAR345 data collection REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing