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Crystal structure of fructose-1,6-bisphosphatase from E.coli GlpX
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 Na Hepes pH 7.5, 10mM Fructose-6-phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.5 50.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.381 α = 90 b = 91.381 β = 90 c = 86.463 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++ 2005-06-10 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 2.1 50 99.8 0.073 30.5 9.2 21967 21967
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 2.1 2.18 98.1 0.525 3 8 2123
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 2.1 39.07 20839 20839 1125 99.61 0.19104 0.19104 0.18808 0.185 0.24985 0.2441 RANDOM 43.85
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] -1.7 -1.7 3.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.086 r_dihedral_angle_3_deg 17.644 r_dihedral_angle_4_deg 17.071 r_dihedral_angle_1_deg 6.759 r_scangle_it 4.315 r_scbond_it 2.749 r_mcangle_it 1.874 r_angle_refined_deg 1.643 r_mcbond_it 1.126 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.086 r_dihedral_angle_3_deg 17.644 r_dihedral_angle_4_deg 17.071 r_dihedral_angle_1_deg 6.759 r_scangle_it 4.315 r_scbond_it 2.749 r_mcangle_it 1.874 r_angle_refined_deg 1.643 r_mcbond_it 1.126 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.241 r_nbd_refined 0.215 r_symmetry_hbond_refined 0.206 r_xyhbond_nbd_refined 0.173 r_chiral_restr 0.114 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 2380 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection CrystalClear data reduction CrystalClear data scaling MOLREP phasing