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Crystal structure of the fructose-1,6-bisphosphatase GlpX from E.coli in complex with inorganic phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NI9 PDB entry 1NI9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 28% PEG 400, 0.2M CaCl2, 0.1M Hepes pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.5 50.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.348 α = 90 b = 91.348 β = 90 c = 86.366 γ = 90
Symmetry Space Group P 4 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2005-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.81 50 99.3 0.056 44.8 12 33731 33731
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.81 1.87 92.9 0.55 3 4.7 3105
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 PDB entry 1NI9 1.85 40.86 30207 30207 1593 99.85 0.19175 0.19175 0.1893 0.1861 0.23922 0.2372 RANDOM 35.743
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] -1.06 -1.06 2.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.674 r_dihedral_angle_4_deg 15.946 r_dihedral_angle_3_deg 15.055 r_dihedral_angle_1_deg 6.44 r_scangle_it 4.383 r_scbond_it 2.884 r_mcangle_it 1.884 r_angle_refined_deg 1.498 r_mcbond_it 1.213 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.674 r_dihedral_angle_4_deg 15.946 r_dihedral_angle_3_deg 15.055 r_dihedral_angle_1_deg 6.44 r_scangle_it 4.383 r_scbond_it 2.884 r_mcangle_it 1.884 r_angle_refined_deg 1.498 r_mcbond_it 1.213 r_nbtor_refined 0.302 r_nbd_refined 0.21 r_xyhbond_nbd_refined 0.178 r_symmetry_vdw_refined 0.176 r_symmetry_hbond_refined 0.148 r_chiral_restr 0.112 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 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 2362 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection CrystalClear data reduction CrystalClear data scaling MOLREP phasing