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Crystal structure of human phosphoglycerate mutase family member 5 (PGAM5) in its enzymatically active dodecameric form induced by the presence of the N-terminal WDPNWD motif
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MXO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.7 293 18% PEG 3350 and 0.1 M MES, pH 5.7
Crystal Properties Matthews coefficient Solvent content 3.27 62.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.215 α = 90 b = 141.403 β = 90 c = 183.12 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 6M 2011-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97630 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 3.1 41.03 94.3 0.271 0.101 6.8 7 18243 55.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.27 96.2 0.993 0.373 2 6.9
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 3MXO 3.1 41.03 17300 933 92.4 0.22793 0.22648 0.2289 0.25553 0.258 RANDOM 50.597
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] 0.49 1.02 -1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.083 r_dihedral_angle_3_deg 15.347 r_dihedral_angle_4_deg 13.027 r_dihedral_angle_1_deg 6.308 r_long_range_B_refined 2.385 r_long_range_B_other 2.385 r_mcangle_it 1.156 r_mcangle_other 1.156 r_angle_refined_deg 1.104 r_scangle_other 0.881
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.083 r_dihedral_angle_3_deg 15.347 r_dihedral_angle_4_deg 13.027 r_dihedral_angle_1_deg 6.308 r_long_range_B_refined 2.385 r_long_range_B_other 2.385 r_mcangle_it 1.156 r_mcangle_other 1.156 r_angle_refined_deg 1.104 r_scangle_other 0.881 r_angle_other_deg 0.779 r_mcbond_it 0.623 r_mcbond_other 0.623 r_scbond_it 0.466 r_scbond_other 0.462 r_chiral_restr 0.066 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 5062 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing