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Crystal structure of pyruvate kinase from Pyrobaculum aerophilum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PKL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.2 294 17% PEG 1500, 100mM Tris pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3.05 59.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.3 α = 90 b = 107.4 β = 110.5 c = 105 γ = 90
Symmetry Space Group C 1 2 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 CCD MARMOSAIC 300 mm CCD 2006-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.000 APS 22-ID
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 2.2 39 99.7 0.053 33.3 3.6 60944 60944 47.6
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 2.2 2.28 98.3 0.403 3.5 3.3 5983
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1PKL 2.2 39 60943 60943 3110 99.41 0.208 0.208 0.206 0.2041 0.247 0.2485 RANDOM 46.1
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] 0.58 -0.78 -0.07 -1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.79 r_dihedral_angle_4_deg 15.921 r_dihedral_angle_3_deg 15.654 r_dihedral_angle_1_deg 5.977 r_scangle_it 3.264 r_scbond_it 2.089 r_mcangle_it 1.371 r_angle_refined_deg 1.37 r_mcbond_it 0.83 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.79 r_dihedral_angle_4_deg 15.921 r_dihedral_angle_3_deg 15.654 r_dihedral_angle_1_deg 5.977 r_scangle_it 3.264 r_scbond_it 2.089 r_mcangle_it 1.371 r_angle_refined_deg 1.37 r_mcbond_it 0.83 r_nbtor_refined 0.3 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.176 r_xyhbond_nbd_refined 0.156 r_symmetry_hbond_refined 0.13 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6701 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 15
Software Software Software Name Purpose MAR345 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling