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Crystal structure of Escherichia coli SeMet substituted Glycerol-3-phosphate Dehydrogenase in complex with DHAP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 0.1M di-Ammonium hydrogen phosphate, 0.1M Bicine, 12% w/v PEG 6000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal Properties Matthews coefficient Solvent content 2.75 55.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.916 α = 90 b = 114.142 β = 90 c = 193.591 γ = 90
Symmetry Space Group I 2 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 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.97928, 0.97947, 0.97181 APS 22-ID
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 1.96 50 96.5 0.113 13.2 6.3 87054
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) 1.96 2.02 80.6 0.614 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.96 10 77725 4086 100 0.2136 0.21098 0.2201 0.26292 0.2642 RANDOM 44.138
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] 0.68 1.56 -2.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.529 r_dihedral_angle_3_deg 20.095 r_dihedral_angle_4_deg 18.437 r_dihedral_angle_1_deg 6.943 r_scangle_it 4.923 r_scbond_it 3.291 r_angle_refined_deg 2.354 r_mcangle_it 2.305 r_mcbond_it 1.55 r_nbtor_refined 0.327
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.529 r_dihedral_angle_3_deg 20.095 r_dihedral_angle_4_deg 18.437 r_dihedral_angle_1_deg 6.943 r_scangle_it 4.923 r_scbond_it 3.291 r_angle_refined_deg 2.354 r_mcangle_it 2.305 r_mcbond_it 1.55 r_nbtor_refined 0.327 r_nbd_refined 0.25 r_symmetry_vdw_refined 0.198 r_xyhbond_nbd_refined 0.173 r_chiral_restr 0.161 r_symmetry_hbond_refined 0.123 r_bond_refined_d 0.024 r_gen_planes_refined 0.01 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7934 Nucleic Acid Atoms Solvent Atoms 277 Heterogen Atoms 434
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction