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Crystal structure of Leishmania major fructose-1,6-bisphosphatase in T-state.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FBP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 290.15 19% w/v PEG 3,350, 5% glycerol, 79% well buffer (0.05 M citric acid, 0.05 M Bis-Tris propane)
Crystal Properties Matthews coefficient Solvent content 2.24 44.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.59 α = 90 b = 109.25 β = 90 c = 140.51 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 PIXEL DECTRIS PILATUS3 S 6M 2014-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9700 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.62 70.25 99.9 12.4 5.5 42513
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 2.62 2.714 0.77
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 5FBP 2.62 70.25 40367 2147 99.75 0.19015 0.18874 0.1938 0.21634 0.2213 RANDOM 56.203
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] -2.87 1.06 1.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.058 r_dihedral_angle_4_deg 15.674 r_dihedral_angle_3_deg 15.12 r_long_range_B_other 7.634 r_long_range_B_refined 7.632 r_dihedral_angle_1_deg 6.149 r_scangle_other 5.245 r_mcangle_other 4.206 r_mcangle_it 4.205 r_scbond_it 3.271
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.058 r_dihedral_angle_4_deg 15.674 r_dihedral_angle_3_deg 15.12 r_long_range_B_other 7.634 r_long_range_B_refined 7.632 r_dihedral_angle_1_deg 6.149 r_scangle_other 5.245 r_mcangle_other 4.206 r_mcangle_it 4.205 r_scbond_it 3.271 r_scbond_other 3.27 r_mcbond_it 2.603 r_mcbond_other 2.595 r_angle_refined_deg 1.416 r_angle_other_deg 1.278 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_bond_other_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10007 Nucleic Acid Atoms Solvent Atoms 114 Heterogen Atoms 158
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing