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Crystal structure of Leishmania major fructose-1,6-bisphosphatase in holo 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, HANGING DROP 6 290.15 20% w/v PEG 3,350,0.05 M citric acid, 0.05 M Bis-Tris propane
Crystal Properties Matthews coefficient Solvent content 2.12 42.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.01 α = 90 b = 104.15 β = 90 c = 137.74 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 2012-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 2.8 55.14 100 0.054 12.3 13.7 33215
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 2.8 2.9 100 0.74 3.9
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 2.8 55.14 31538 1677 99.79 0.19549 0.19306 0.1984 0.24125 0.2444 RANDOM 33.427
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] 0.06 -2.16 2.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.908 r_dihedral_angle_4_deg 19.484 r_dihedral_angle_3_deg 16.93 r_long_range_B_refined 9.456 r_long_range_B_other 9.456 r_dihedral_angle_1_deg 6.282 r_scangle_other 4.342 r_mcangle_it 4.278 r_mcangle_other 4.278 r_scbond_it 2.573
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.908 r_dihedral_angle_4_deg 19.484 r_dihedral_angle_3_deg 16.93 r_long_range_B_refined 9.456 r_long_range_B_other 9.456 r_dihedral_angle_1_deg 6.282 r_scangle_other 4.342 r_mcangle_it 4.278 r_mcangle_other 4.278 r_scbond_it 2.573 r_scbond_other 2.572 r_mcbond_it 2.497 r_mcbond_other 2.493 r_angle_other_deg 1.703 r_angle_refined_deg 1.65 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_bond_other_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.006 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 9913 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing