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Crystal structure of Possible 1-phosphofructokinase (EC 2.7.1.56) (tm0828) from Thermotoga Maritima at 2.46 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 293 16% PEG-8000, 0.08M sodium cacodylate, 0.16M magnesium acetate tetrahydrate, 20% glyerol anhyrous , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K, pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.94 57.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.796 α = 90 b = 115.796 β = 90 c = 124.828 γ = 90
Symmetry Space Group P 41 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 CCD ADSC QUANTUM 315 FLAT MIRROR 2002-06-17 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.885567,0.976224 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.4 29.2 99.5 0.109 0.109 5.9 6.3 31322
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.46 2.52 95 0.633 0.633 1.2 3.5
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.46 28.49 29692 1595 99.4 0.193 0.1966 0.24 0.2413 RANDOM 31.77
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] 1.31 1.31 -2.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.829 r_dihedral_angle_3_deg 17.005 r_dihedral_angle_4_deg 15.688 r_scangle_it 6.864 r_dihedral_angle_1_deg 6.194 r_scbond_it 5.131 r_mcangle_it 2.525 r_mcbond_it 1.719 r_angle_refined_deg 1.274 r_angle_other_deg 0.825
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.829 r_dihedral_angle_3_deg 17.005 r_dihedral_angle_4_deg 15.688 r_scangle_it 6.864 r_dihedral_angle_1_deg 6.194 r_scbond_it 5.131 r_mcangle_it 2.525 r_mcbond_it 1.719 r_angle_refined_deg 1.274 r_angle_other_deg 0.825 r_mcbond_other 0.391 r_nbd_refined 0.204 r_symmetry_vdw_other 0.204 r_nbd_other 0.183 r_nbtor_refined 0.181 r_symmetry_hbond_refined 0.159 r_symmetry_vdw_refined 0.158 r_xyhbond_nbd_refined 0.148 r_nbtor_other 0.086 r_chiral_restr 0.073 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 5013 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling SnB phasing MLPHARE phasing SOLVE phasing