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Crystal structure of 2-dehydro-3- deoxygluconokinase (EC 2.7.1.45) (tm0067) from THERMOTOGA MARITIMA at 2.05 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 7 273 50.0% PEG-200, 0.1M Tris pH 7.0 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 2.41 48.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.993 α = 90 b = 120.993 β = 90 c = 260.3 γ = 120
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 4 2001-07-01 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.979413, 0.904964, 0.979150 SSRL BL9-2
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 2.05 49.69 98.2 0.077 0.077 6.6 4.6 45533 27.8
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 2.05 2.16 89.9 89.9 0.381 0.381 1.9 2.8
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-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 MAD THROUGHOUT 2.05 48.63 44437 1069 98.07 0.177 0.177 0.176 0.1869 0.23 0.2392 RANDOM 28.282
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] 0.74 0.37 0.74 -1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.363 r_dihedral_angle_3_deg 15.112 r_dihedral_angle_4_deg 14.239 r_dihedral_angle_1_deg 6.892 r_scangle_it 6.783 r_scbond_it 5.306 r_mcangle_it 2.974 r_mcbond_it 2.202 r_angle_refined_deg 1.55 r_angle_other_deg 0.835
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.363 r_dihedral_angle_3_deg 15.112 r_dihedral_angle_4_deg 14.239 r_dihedral_angle_1_deg 6.892 r_scangle_it 6.783 r_scbond_it 5.306 r_mcangle_it 2.974 r_mcbond_it 2.202 r_angle_refined_deg 1.55 r_angle_other_deg 0.835 r_mcbond_other 0.708 r_symmetry_vdw_refined 0.415 r_symmetry_vdw_other 0.35 r_symmetry_metal_ion_refined 0.348 r_metal_ion_refined 0.306 r_nbd_refined 0.211 r_nbtor_refined 0.183 r_nbd_other 0.178 r_xyhbond_nbd_refined 0.152 r_symmetry_hbond_refined 0.12 r_chiral_restr 0.093 r_nbtor_other 0.086 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5040 Nucleic Acid Atoms Solvent Atoms 394 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 CCP4 phasing SOLVE phasing SHARP phasing