☰ Navigation Tabs
Crystal Structure of the Bacillus stearothermophilus Phosphofructokinase Mutant D12A in Complex with PEP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3U39
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 289 0.1 M sodium citrate tribasic dehydrate pH 5.6, 20% v/v 2-propanol, 20% w/v polyethylene glycol 4,000, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.62 53.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.65 α = 90 b = 112.96 β = 90 c = 131.04 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 IMAGE PLATE RIGAKU RAXIS IV++ MIRRORS 2009-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
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 65.52 97 0.053 13.3 3.61 94461 29
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 2.07 78.2 0.389 2.7 2.88
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3U39 2 56.7 94460 94460 4715 97 0.191 0.189 0.1954 0.235 0.2394 RANDOM 47.67
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] -0.11 0.39 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.316 r_dihedral_angle_3_deg 15.254 r_dihedral_angle_4_deg 14.146 r_dihedral_angle_1_deg 8.92 r_scangle_it 2.497 r_scbond_it 1.621 r_angle_refined_deg 1.355 r_mcangle_it 1.165 r_angle_other_deg 0.914 r_mcbond_it 0.685
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.316 r_dihedral_angle_3_deg 15.254 r_dihedral_angle_4_deg 14.146 r_dihedral_angle_1_deg 8.92 r_scangle_it 2.497 r_scbond_it 1.621 r_angle_refined_deg 1.355 r_mcangle_it 1.165 r_angle_other_deg 0.914 r_mcbond_it 0.685 r_symmetry_vdw_other 0.257 r_nbd_refined 0.206 r_nbd_other 0.202 r_nbtor_refined 0.17 r_symmetry_hbond_refined 0.168 r_symmetry_vdw_refined 0.157 r_xyhbond_nbd_refined 0.155 r_mcbond_other 0.133 r_nbtor_other 0.086 r_chiral_restr 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9482 Nucleic Acid Atoms Solvent Atoms 626 Heterogen Atoms 40
Software Software Software Name Purpose d*TREK data scaling d*TREK data reduction PHASER phasing REFMAC refinement PDB_EXTRACT data extraction