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Klebsiella pneumoniae BlrP1 with FMN and cyclic diGMP, no metal ions
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 2.33 47.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.43 α = 90 b = 96.53 β = 90 c = 127.07 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 2.6 46.56 96.4 0.104 13.4 5.4 25028 25028
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 2.6 2.7 96.4 0.352 5.4
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 2.6 46.56 25028 25028 1390 99.41 0.25904 0.25904 0.25758 0.2557 0.28577 0.2819 RANDOM 26.859
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] 0.67 -1.73 1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.988 r_dihedral_angle_3_deg 14.245 r_dihedral_angle_4_deg 12.604 r_dihedral_angle_1_deg 5.691 r_angle_refined_deg 1.368 r_scangle_it 0.913 r_mcangle_it 0.554 r_scbond_it 0.521 r_mcbond_it 0.318 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.988 r_dihedral_angle_3_deg 14.245 r_dihedral_angle_4_deg 12.604 r_dihedral_angle_1_deg 5.691 r_angle_refined_deg 1.368 r_scangle_it 0.913 r_mcangle_it 0.554 r_scbond_it 0.521 r_mcbond_it 0.318 r_nbtor_refined 0.302 r_symmetry_hbond_refined 0.198 r_xyhbond_nbd_refined 0.16 r_nbd_refined 0.157 r_symmetry_vdw_refined 0.134 r_chiral_restr 0.073 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 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_refined 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 5874 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 154
Software Software Software Name Purpose MAR345 data collection REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing