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Crystal structure of Glycerol-3-phosphate Dehydrogenase from Escherichia coli
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 0.1 M di-Ammonium hydrogen phosphate, 0.1 M Tris-HCl pH 8.5, 12 % w/v PEG MME 550, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal Properties Matthews coefficient Solvent content 2.75 55.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.791 α = 90 b = 114.097 β = 90 c = 192.801 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 CCD MARMOSAIC 225 mm CCD M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MARMOSAIC 300 mm CCD M MAD 3 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9803 SLS X10SA 2 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 1,2 1.7 50 99.4 0.061 11.8 9 136571
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) 1.7 1.76 98.1 0.712 5.1
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 1.75 10 118338 6272 99.54 0.20564 0.20381 0.215 0.23998 0.2495 RANDOM 30.653
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] 0.01 0.02 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.356 r_dihedral_angle_3_deg 18.183 r_dihedral_angle_4_deg 17.041 r_dihedral_angle_1_deg 14.085 r_scangle_it 6.223 r_scbond_it 4.344 r_mcangle_it 3.034 r_mcbond_it 2.108 r_angle_refined_deg 1.74 r_nbtor_refined 0.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.356 r_dihedral_angle_3_deg 18.183 r_dihedral_angle_4_deg 17.041 r_dihedral_angle_1_deg 14.085 r_scangle_it 6.223 r_scbond_it 4.344 r_mcangle_it 3.034 r_mcbond_it 2.108 r_angle_refined_deg 1.74 r_nbtor_refined 0.326 r_symmetry_vdw_refined 0.288 r_nbd_refined 0.253 r_chiral_restr 0.251 r_symmetry_hbond_refined 0.25 r_xyhbond_nbd_refined 0.167 r_gen_planes_refined 0.019 r_bond_refined_d 0.011 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 7997 Nucleic Acid Atoms Solvent Atoms 476 Heterogen Atoms 419
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing SOLVE phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction