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Crystal structure of 2-keto-3-deoxygluconate kinase (form 1) from Sulfolobus Tokodaii
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 0.1M Tris-HCl, 5% PEG1000, 40% PEG300, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.459 50.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.666 α = 90 b = 149.103 β = 90 c = 161.096 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 CCD ADSC QUANTUM 210 2004-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.000 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.8 49.104 99.8 51243 51243
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 99.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.8 50 45793 45793 5109 99.85 0.18811 0.18811 0.17894 0.27048 RANDOM 32.923
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] -0.78 -0.87 1.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.033 r_scangle_it 3.141 r_scbond_it 1.872 r_angle_refined_deg 1.726 r_mcangle_it 1.199 r_mcbond_it 0.623 r_nbd_refined 0.237 r_symmetry_vdw_refined 0.231 r_xyhbond_nbd_refined 0.173 r_symmetry_hbond_refined 0.146
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.033 r_scangle_it 3.141 r_scbond_it 1.872 r_angle_refined_deg 1.726 r_mcangle_it 1.199 r_mcbond_it 0.623 r_nbd_refined 0.237 r_symmetry_vdw_refined 0.231 r_xyhbond_nbd_refined 0.173 r_symmetry_hbond_refined 0.146 r_chiral_restr 0.121 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined 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 14456 Nucleic Acid Atoms Solvent Atoms 380 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction CCP4 data scaling AMoRE phasing