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Crystal structure of fructose bisphosphate aldolase from Bartonella henselae, bound to fructose bisphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KX6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 290 0.2 M NAOAC, 0.1 M TRIS PH 8.5, 30% PEG 4000, protein AT 21 MG/ML, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.3 46.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.39 α = 90 b = 127.71 β = 90 c = 157.63 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 100 CCD ADSC QUANTUM Q315 2010-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97740 ALS 5.0.1
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 2.35 47.89 100 0.099 8.9 61687 61670 -3 35.97
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 2.35 2.41 99.9 0.553 4.2 8.4 4533
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 3KX6 2.35 47.89 61687 61429 3122 0.179 0.179 0.177 0.1785 0.222 0.2224 RANDOM 26.95
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] 0.04 0.87 -0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.787 r_dihedral_angle_4_deg 17.287 r_dihedral_angle_3_deg 14.706 r_dihedral_angle_1_deg 5.775 r_scangle_it 2.281 r_scbond_it 1.352 r_angle_refined_deg 1.18 r_angle_other_deg 0.871 r_mcangle_it 0.769 r_mcbond_it 0.403
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.787 r_dihedral_angle_4_deg 17.287 r_dihedral_angle_3_deg 14.706 r_dihedral_angle_1_deg 5.775 r_scangle_it 2.281 r_scbond_it 1.352 r_angle_refined_deg 1.18 r_angle_other_deg 0.871 r_mcangle_it 0.769 r_mcbond_it 0.403 r_mcbond_other 0.102 r_chiral_restr 0.062 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 10241 Nucleic Acid Atoms Solvent Atoms 498 Heterogen Atoms 76
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling