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Crystal structure of phosphoglucose isomerase from Pyrococcus furiosus in complex with gluconate 6-phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QXJ PDB entry 1QXJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 295 25% PEG 4000, 0.2M ammonium acetate, 0.1 M sodium acetate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.3 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36 α = 73.7 b = 39.7 β = 78.5 c = 74.7 γ = 72.6
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 2003-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
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 1.8 36.8 93.5 0.056 8.8 2.7 32924 24.8
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) 1.8 1.86 90 0.355 2.7 2.7 3174
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION Simple refinement THROUGHOUT PDB entry 1QXJ 1.8 15 32520 30880 1640 93.48 0.22 0.22 0.218 0.266 0.2566 RANDOM 33.652
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] 1.75 -0.83 -0.4 -0.09 1.74 -1.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.326 r_dihedral_angle_1_deg 5.013 r_scangle_it 3.592 r_scbond_it 2.282 r_angle_refined_deg 1.723 r_mcangle_it 1.438 r_mcbond_it 0.822 r_symmetry_hbond_refined 0.279 r_nbd_refined 0.222 r_symmetry_vdw_refined 0.182
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.326 r_dihedral_angle_1_deg 5.013 r_scangle_it 3.592 r_scbond_it 2.282 r_angle_refined_deg 1.723 r_mcangle_it 1.438 r_mcbond_it 0.822 r_symmetry_hbond_refined 0.279 r_nbd_refined 0.222 r_symmetry_vdw_refined 0.182 r_xyhbond_nbd_refined 0.176 r_chiral_restr 0.113 r_bond_refined_d 0.016 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3004 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction CrystalClear data scaling