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Klebsiella pneumoniae BlrP1 pH 4.5 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 2.38 48.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69 α = 90 b = 96.9 β = 90 c = 128.5 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 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 0.998 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 2.4 15 95.1 0.104 12.2 4.7 32027 32027
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 2.4 2.5 80.6 0.352 3.2 3.8
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 SAD THROUGHOUT 2.4 15 32027 32027 1696 100 0.23209 0.23209 0.22967 0.2453 0.27709 0.2891 RANDOM 24.872
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] -0.46 -2.07 2.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.203 r_dihedral_angle_3_deg 14.981 r_dihedral_angle_4_deg 10.467 r_dihedral_angle_1_deg 5.464 r_angle_refined_deg 1.323 r_scangle_it 0.533 r_nbtor_refined 0.301 r_mcangle_it 0.297 r_scbond_it 0.294 r_symmetry_vdw_refined 0.182
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.203 r_dihedral_angle_3_deg 14.981 r_dihedral_angle_4_deg 10.467 r_dihedral_angle_1_deg 5.464 r_angle_refined_deg 1.323 r_scangle_it 0.533 r_nbtor_refined 0.301 r_mcangle_it 0.297 r_scbond_it 0.294 r_symmetry_vdw_refined 0.182 r_mcbond_it 0.169 r_nbd_refined 0.155 r_xyhbond_nbd_refined 0.143 r_metal_ion_refined 0.142 r_symmetry_hbond_refined 0.134 r_chiral_restr 0.072 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_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 Atoms Number Protein Atoms 6163 Nucleic Acid Atoms Solvent Atoms 406 Heterogen Atoms 156
Software Software Software Name Purpose MAR345 data collection autoSHARP phasing REFMAC refinement XDS data reduction XSCALE data scaling