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The X-ray structure of human M190I phosphoglycerate kinase 1 mutant
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 PEG MME 30% w/v, Bis Tris 0.1 M pH=7
Crystal Properties Matthews coefficient Solvent content 2.14 42.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.363 α = 90 b = 91.104 β = 90 c = 109.01 γ = 90
Symmetry Space Group P 21 21 21
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 RAYONIX MX-225 2016-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.3 0.894 BESSY 14.3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.05 69.91 99.7 13.15 5.99 24685
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 MOLECULAR REPLACEMENT THROUGHOUT 2.05 69.91 23510 1190 99.73 0.17861 0.17623 0.1865 0.22554 0.231 RANDOM 22.582
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] -0.32 1.8 -1.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.478 r_dihedral_angle_4_deg 20.027 r_dihedral_angle_3_deg 15.28 r_long_range_B_refined 9.278 r_long_range_B_other 9.277 r_dihedral_angle_1_deg 6.723 r_scangle_other 3.711 r_mcangle_it 2.506 r_mcangle_other 2.506 r_scbond_it 2.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.478 r_dihedral_angle_4_deg 20.027 r_dihedral_angle_3_deg 15.28 r_long_range_B_refined 9.278 r_long_range_B_other 9.277 r_dihedral_angle_1_deg 6.723 r_scangle_other 3.711 r_mcangle_it 2.506 r_mcangle_other 2.506 r_scbond_it 2.38 r_scbond_other 2.379 r_angle_refined_deg 1.953 r_mcbond_other 1.663 r_mcbond_it 1.662 r_angle_other_deg 1.047 r_chiral_restr 0.127 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 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 3110 Nucleic Acid Atoms Solvent Atoms 282 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing