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Structure of the PGK1 from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WZB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M Na/K PO4, 20% PEG 3,350
Crystal Properties Matthews coefficient Solvent content 2.32 46.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.591 α = 90 b = 70.058 β = 90 c = 95.681 γ = 90
Symmetry Space Group P 21 21 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 EIGER X 9M 2021-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 1.18075 CLSI 08ID-1
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 1.95 47.84 99.8 0.094 12.9 6.1 30843
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 1.95 2 0.742
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.95 46.3 30812 1552 99.744 0.236 0.2337 0.2864 0.2699 37.359
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] -2.378 3.899 -1.522
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 11.974 r_dihedral_angle_3_deg 11.836 r_dihedral_angle_1_deg 5.795 r_dihedral_angle_2_deg 5.689 r_lrange_it 4.137 r_lrange_other 3.986 r_scangle_it 2.317 r_scangle_other 2.317 r_mcangle_it 2.228 r_mcangle_other 2.227
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 11.974 r_dihedral_angle_3_deg 11.836 r_dihedral_angle_1_deg 5.795 r_dihedral_angle_2_deg 5.689 r_lrange_it 4.137 r_lrange_other 3.986 r_scangle_it 2.317 r_scangle_other 2.317 r_mcangle_it 2.228 r_mcangle_other 2.227 r_mcbond_it 1.343 r_mcbond_other 1.343 r_scbond_it 1.328 r_scbond_other 1.327 r_angle_refined_deg 0.898 r_angle_other_deg 0.326 r_nbd_refined 0.199 r_symmetry_nbd_other 0.177 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.143 r_symmetry_xyhbond_nbd_refined 0.133 r_nbd_other 0.128 r_symmetry_nbtor_other 0.076 r_symmetry_nbd_refined 0.075 r_chiral_restr 0.043 r_symmetry_xyhbond_nbd_other 0.006 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3116 Nucleic Acid Atoms Solvent Atoms 288 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing