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Crystal structure of Leishmania major fructose-1,6-bisphosphatase in apo form.
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 5 290.15 20% w/v PEG 3,350, 0.05 M citric acid, 0.05 M Bis-Tris propane
Crystal Properties Matthews coefficient Solvent content 2.46 49.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.26 α = 90 b = 162.56 β = 90 c = 170.13 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 PILATUS 300K 2012-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
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 2.41 58.77 99.4 0.094 9.2 4.9 59755
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.41 2.496 99.8 2.9
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 2.41 58.77 56736 3019 99.23 0.18886 0.18699 0.1941 0.22536 0.231 RANDOM 66.097
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] -0.61 0.26 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.204 r_dihedral_angle_4_deg 17.38 r_dihedral_angle_3_deg 16.366 r_long_range_B_other 13.458 r_long_range_B_refined 13.454 r_scangle_other 11.003 r_scbond_it 8.082 r_scbond_other 8.081 r_mcangle_it 7.648 r_mcangle_other 7.647
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.204 r_dihedral_angle_4_deg 17.38 r_dihedral_angle_3_deg 16.366 r_long_range_B_other 13.458 r_long_range_B_refined 13.454 r_scangle_other 11.003 r_scbond_it 8.082 r_scbond_other 8.081 r_mcangle_it 7.648 r_mcangle_other 7.647 r_dihedral_angle_1_deg 6.081 r_mcbond_other 5.58 r_mcbond_it 5.579 r_angle_refined_deg 1.495 r_angle_other_deg 1.473 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_bond_other_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.005 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 9747 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing