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Structure of E. coli GlpX with its substrate fructose 1,6-bisphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NI9 PDB code 1NI9 protein atoms
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 26% PEG400, 0.15M CaCl2, 0.1M Hepes pH 7.5, 2.5 % PEG3350, 20mM MgCl2, 10mM Fructose 1,6 bis phosphate, 2mM L-cysteine, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.46 50.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.296 α = 90 b = 91.296 β = 90 c = 84.913 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 Mirrors 2008-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54178
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 1.85 50 100 0.06 40.1 13.5 31313 31306
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 1.85 1.92 100 0.464 7.2 13.1
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 PDB code 1NI9 protein atoms 1.85 28.65 29726 1578 99.93 0.17733 0.17523 0.1748 0.21634 0.2162 RANDOM 26.24
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] -0.01 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.188 r_dihedral_angle_4_deg 18.462 r_dihedral_angle_3_deg 14.612 r_dihedral_angle_1_deg 5.9 r_scangle_it 4.532 r_scbond_it 2.95 r_mcangle_it 1.685 r_angle_refined_deg 1.627 r_mcbond_it 1.09 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.188 r_dihedral_angle_4_deg 18.462 r_dihedral_angle_3_deg 14.612 r_dihedral_angle_1_deg 5.9 r_scangle_it 4.532 r_scbond_it 2.95 r_mcangle_it 1.685 r_angle_refined_deg 1.627 r_mcbond_it 1.09 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.247 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.182 r_chiral_restr 0.119 r_symmetry_hbond_refined 0.1 r_metal_ion_refined 0.049 r_bond_refined_d 0.02 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_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 2368 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing