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Geobacillus stearothermophilus 6-phosphogluconate dehydrogenase with bound 6- phosphogluconate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IYO PDB ENTRY 2IYO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.4 0.2 M LITHIUM SULFATE, 2.2 M AMMONIUM SULFATE, pH 7.4
Crystal Properties Matthews coefficient Solvent content 2.8 55.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.035 α = 90 b = 119.965 β = 90 c = 142.827 γ = 90
Symmetry Space Group P 21 21 21
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 CCD TORODIAL FOCUSING MIRROR 2007-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.3 92.06 100 0.12 14.1 6.9 52157
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.42 99.9 3.2 5.8
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 2IYO 2.3 71.43 49316 2618 99.9 0.185 0.182 0.1814 0.234 0.2307 RANDOM 26.23
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] 2.2 -2.37 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.049 r_dihedral_angle_4_deg 18.141 r_dihedral_angle_3_deg 16.96 r_dihedral_angle_1_deg 5.46 r_scangle_it 2.43 r_scbond_it 1.556 r_angle_refined_deg 1.389 r_mcangle_it 1.063 r_mcbond_it 0.617 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.049 r_dihedral_angle_4_deg 18.141 r_dihedral_angle_3_deg 16.96 r_dihedral_angle_1_deg 5.46 r_scangle_it 2.43 r_scbond_it 1.556 r_angle_refined_deg 1.389 r_mcangle_it 1.063 r_mcbond_it 0.617 r_nbtor_refined 0.303 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.161 r_symmetry_hbond_refined 0.153 r_symmetry_vdw_refined 0.147 r_chiral_restr 0.101 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7293 Nucleic Acid Atoms Solvent Atoms 347 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing