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HUMAN ERYTHROCYTE PYRUVATE KINASE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PKN PDB ENTRY 1PKN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 RECOMBINANT WILD-TYPE RPK WAS CRYSTALLIZED USING THE VAPOR DIFFUSION METHOD AT 22 C. WELL SOLUTIONS CONSISTED OF 50 MM MES/KOH, PH 6.4, 10 MM MNSO4, AND 10-14% W/V PEG8000. HANGING DROPS WERE FORMED BY MIXING EQUAL VOLUMES OF 12 MG/ML PROTEIN IN 50 MM KCL, 5 MM FBP, 5 MM PHOSPHOGLYCOLATE, 20 MM POTASSIUM PHOSPHATE, PH 7.0, AND WELL SOLUTIONS.
Crystal Properties Matthews coefficient Solvent content 2.5 50.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.413 α = 90 b = 172.058 β = 92.46 c = 85.512 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF ESRF ID14-2
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 2.7 20 95.9 0.08 13.4 2.1 55091
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 2.7 2.7 86.5 0.24 2.4 2.1
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 PDB ENTRY 1PKN 2.73 20 52174 2780 96.3 0.229 0.227 0.2213 0.271 0.2641 RANDOM 40.86
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] -0.14 0.12 0.2 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.011 r_dihedral_angle_4_deg 23.116 r_dihedral_angle_3_deg 20.809 r_dihedral_angle_1_deg 5.423 r_scangle_it 2.564 r_scbond_it 1.546 r_angle_refined_deg 1.513 r_mcangle_it 0.785 r_symmetry_vdw_refined 0.54 r_mcbond_it 0.399
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.011 r_dihedral_angle_4_deg 23.116 r_dihedral_angle_3_deg 20.809 r_dihedral_angle_1_deg 5.423 r_scangle_it 2.564 r_scbond_it 1.546 r_angle_refined_deg 1.513 r_mcangle_it 0.785 r_symmetry_vdw_refined 0.54 r_mcbond_it 0.399 r_nbtor_refined 0.322 r_symmetry_hbond_refined 0.315 r_nbd_refined 0.257 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.095 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15423 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 124
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing