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Klebsiella pneumoniae BlrP1 pH 6 manganese/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 2.34 47.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.45 α = 90 b = 97.09 β = 90 c = 127.17 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 0.98407 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 2.05 48.54 93.2 0.066 13.6 4.3 49739 49739
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 2.05 2.15 81.9 0.386 3.6 3.3
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 2.05 48.54 49739 49739 2618 97.14 0.23105 0.23105 0.22895 0.2319 0.27151 0.2754 RANDOM 38.857
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 -3 3.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.733 r_dihedral_angle_4_deg 15.725 r_dihedral_angle_3_deg 14.442 r_dihedral_angle_1_deg 8.461 r_angle_refined_deg 1.596 r_scangle_it 1.48 r_scbond_it 0.971 r_angle_other_deg 0.868 r_mcangle_it 0.621 r_mcbond_it 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.733 r_dihedral_angle_4_deg 15.725 r_dihedral_angle_3_deg 14.442 r_dihedral_angle_1_deg 8.461 r_angle_refined_deg 1.596 r_scangle_it 1.48 r_scbond_it 0.971 r_angle_other_deg 0.868 r_mcangle_it 0.621 r_mcbond_it 0.55 r_symmetry_hbond_refined 0.204 r_xyhbond_nbd_refined 0.193 r_symmetry_vdw_other 0.187 r_nbd_refined 0.182 r_nbtor_refined 0.176 r_symmetry_vdw_refined 0.176 r_xyhbond_nbd_other 0.161 r_nbd_other 0.153 r_chiral_restr 0.136 r_nbtor_other 0.085 r_mcbond_other 0.079 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 6174 Nucleic Acid Atoms Solvent Atoms 346 Heterogen Atoms 158
Software Software Software Name Purpose MAR345 data collection REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing