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Crystal structure of pGI glucosephosphate isomerase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DQR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 25% PEG 3350, 0.2M ammonium acetate, 0.1M Bis-Tris 5.5, 10 mM betaine HCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.24 45.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.806 α = 92.47 b = 72.874 β = 97.82 c = 181.851 γ = 114.57
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r KOHZU: Double Crystal Si(111) 2007-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11587 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.99 89 94.6 0.104 0.104 9.7 2 208294 208294 1 1 23
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.99 2.1 94.6 0.423 0.423 1.7 2 29607
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 1dqr 2.05 89 181581 9609 94.94 0.17227 0.16923 0.1705 0.22952 0.2299 RANDOM 23.059
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] 0.88 -1.16 -0.82 -1.03 -1.09 -1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.219 r_dihedral_angle_4_deg 15.94 r_dihedral_angle_3_deg 15.144 r_dihedral_angle_1_deg 5.797 r_scangle_it 4.577 r_scbond_it 3.045 r_mcangle_it 1.689 r_angle_refined_deg 1.313 r_mcbond_it 0.985 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.219 r_dihedral_angle_4_deg 15.94 r_dihedral_angle_3_deg 15.144 r_dihedral_angle_1_deg 5.797 r_scangle_it 4.577 r_scbond_it 3.045 r_mcangle_it 1.689 r_angle_refined_deg 1.313 r_mcbond_it 0.985 r_chiral_restr 0.095 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25984 Nucleic Acid Atoms Solvent Atoms 3262 Heterogen Atoms 1
Software Software Software Name Purpose Blu-Ice data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling