☰ Navigation Tabs
Crystal Structure of a Phosphofructokinase from Pyrococcus horikoshii OT3 with AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U2X 1U2X molecule A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 20% PEG 3350, 0.2 M Lithium Citrate plus 5 mM ADP Cryoprotected in N-paratone oil., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.24 45.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.464 α = 90 b = 104.19 β = 105.09 c = 70.844 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 CCD ADSC QUANTUM 315 mirrors 2007-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97929 APS 19-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 1.9 50 98.7 0.08 16.7 4.5 75838 74815 23.5
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 1.9 1.97 90.7 0.353 3.2 3.9 6856
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1U2X molecule A 1.9 41.45 74775 71005 3770 98.27 0.17426 0.17161 0.1831 0.2244 RANDOM 29.37
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] -0.05 0.03 0.1 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.107 r_dihedral_angle_4_deg 18.377 r_dihedral_angle_3_deg 15.637 r_dihedral_angle_1_deg 7.542 r_scangle_it 5.917 r_scbond_it 3.545 r_mcangle_it 1.991 r_angle_refined_deg 1.8 r_mcbond_it 1.082 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.107 r_dihedral_angle_4_deg 18.377 r_dihedral_angle_3_deg 15.637 r_dihedral_angle_1_deg 7.542 r_scangle_it 5.917 r_scbond_it 3.545 r_mcangle_it 1.991 r_angle_refined_deg 1.8 r_mcbond_it 1.082 r_nbtor_refined 0.316 r_nbd_refined 0.22 r_symmetry_vdw_refined 0.215 r_chiral_restr 0.165 r_symmetry_hbond_refined 0.153 r_xyhbond_nbd_refined 0.15 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7379 Nucleic Acid Atoms Solvent Atoms 576 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing