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CRYSTAL STRUCTURE OF GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM PIG MUSCLE COMPLEXED WITH ORTHOPHENANTHROLINE AT 1.90 ANGSTROM RESOLUTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GD1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 273 0.005M 1,10-ORTHOPHENANTHROLINE, 0.05M HEPES, PH 8.0, 54.7%(W/V)AMMONIUM SULFATE,0.005 M EDTA, HANGING DROP, TEMPERATURE 277 K
Crystal Properties Matthews coefficient Solvent content 3.03 59.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.48 α = 90 b = 133.52 β = 90 c = 210.32 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 120 PIXEL DECTRIS PILATUS3 2M 2005-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.00 APS 17-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 1.9 43.54 93.6 0.066 12 4.3 87846
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 93.6 0.159 2.7
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 1GD1 1.9 43.54 87846 1319 93.6 0.133 0.132 0.1349 0.2 0.2023 RANDOM 35.4
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] -0.11 0.17 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.357 r_sphericity_free 21.834 r_dihedral_angle_4_deg 18.416 r_dihedral_angle_3_deg 14.811 r_sphericity_bonded 9.266 r_rigid_bond_restr 7.026 r_dihedral_angle_1_deg 7.016 r_long_range_B_refined 5.282 r_long_range_B_other 5.123 r_scangle_other 5.043
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.357 r_sphericity_free 21.834 r_dihedral_angle_4_deg 18.416 r_dihedral_angle_3_deg 14.811 r_sphericity_bonded 9.266 r_rigid_bond_restr 7.026 r_dihedral_angle_1_deg 7.016 r_long_range_B_refined 5.282 r_long_range_B_other 5.123 r_scangle_other 5.043 r_scbond_it 4.634 r_scbond_other 4.634 r_mcangle_it 4.242 r_mcangle_other 4.241 r_mcbond_it 3.98 r_mcbond_other 3.979 r_angle_refined_deg 2.019 r_angle_other_deg 0.959 r_chiral_restr 0.135 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7530 Nucleic Acid Atoms Solvent Atoms 883 Heterogen Atoms 285
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling AMoRE phasing DENZO data reduction