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Crystal structure of phosphorylated mutant of glyceraldehyde 3-phosphate dehydrogenase from human placenta at 3.15A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U8F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.7 293 4M sodium formate, pH 7.7
Crystal Properties Matthews coefficient Solvent content 2.93 58.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.78 α = 90 b = 131.68 β = 90 c = 220.64 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 PIXEL DECTRIS PILATUS3 S 6M mirror 2018-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.953 ESRF ID29
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 3.15 45.39 100 0.2 5.6 5.3 23302
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 3.15 3.23 100 0.15 1.4 5
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 1U8F 3.15 45.39 22126 1161 99.89 0.19627 0.19398 0.1976 0.23937 0.2319 RANDOM 70
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] 4.16 -5.61 1.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.66 r_dihedral_angle_4_deg 20.524 r_dihedral_angle_3_deg 18.581 r_long_range_B_refined 15.552 r_long_range_B_other 15.552 r_scangle_other 9.51 r_mcangle_it 8.541 r_mcangle_other 8.54 r_dihedral_angle_1_deg 7.171 r_scbond_it 5.903
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.66 r_dihedral_angle_4_deg 20.524 r_dihedral_angle_3_deg 18.581 r_long_range_B_refined 15.552 r_long_range_B_other 15.552 r_scangle_other 9.51 r_mcangle_it 8.541 r_mcangle_other 8.54 r_dihedral_angle_1_deg 7.171 r_scbond_it 5.903 r_scbond_other 5.902 r_mcbond_it 5.392 r_mcbond_other 5.392 r_angle_refined_deg 1.399 r_angle_other_deg 0.84 r_chiral_restr 0.056 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7590 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling MOLREP phasing