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The structure of Glucose-6-phosphate isomerase (GPI) from Brucella melitensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WU8 pdb entry 2WU8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 39.92 mg/ml BrmeA.17127.a PW34214, 0.2M calcium chloride dihydrate, 20% PEG3350. Cryoprotection 20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.33 47.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.59 α = 95.42 b = 72.73 β = 91.54 c = 115.25 γ = 110.06
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 MARMOSAIC 225 mm CCD 2012-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.9 95.066 95.1 0.026 27.06 162585 -3 16.591
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 1.9 1.95 80.3 0.059 13.44
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 entry 2WU8 1.9 95.066 162585 8159 95.07 0.1327 0.1308 0.1444 0.1689 0.1797 RANDOM 9.9259
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] -0.33 0.21 0.55 0.25 0.95 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.914 r_dihedral_angle_4_deg 19.359 r_dihedral_angle_3_deg 11.482 r_dihedral_angle_1_deg 5.671 r_scangle_it 2.683 r_scbond_it 1.697 r_angle_refined_deg 1.313 r_mcangle_it 0.98 r_angle_other_deg 0.919 r_mcbond_it 0.565
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.914 r_dihedral_angle_4_deg 19.359 r_dihedral_angle_3_deg 11.482 r_dihedral_angle_1_deg 5.671 r_scangle_it 2.683 r_scbond_it 1.697 r_angle_refined_deg 1.313 r_mcangle_it 0.98 r_angle_other_deg 0.919 r_mcbond_it 0.565 r_mcbond_other 0.166 r_chiral_restr 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16590 Nucleic Acid Atoms Solvent Atoms 2587 Heterogen Atoms 21
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction