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Crystal structure of the apo E. coli xylulose kinase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 Drops containing equal volume of 26 mg/ml protein solution mixed with the precipitant solution containing 1.5 M ammonium sulfate, 50 mM sodium citrate, 1% w/v t-butanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.5 50.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.78 α = 90 b = 112.02 β = 90 c = 138.8 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 110 CCD ADSC QUANTUM 315 Vertical focusing mirror 2004-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.954 SSRL BL9-1
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 2.7 24.88 10.09 29677 29677 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.7 24.88 10
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.7 24.88 28719 27537 1182 96.77 0.20681 0.20482 0.2008 0.25417 0.247 RANDOM 33.31
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] 0.64 -1.1 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.822 r_dihedral_angle_4_deg 19.539 r_dihedral_angle_3_deg 18.38 r_scangle_it 14.419 r_scbond_it 11.706 r_dihedral_angle_1_deg 7.998 r_mcangle_it 7.691 r_mcbond_it 5.435 r_angle_refined_deg 1.706 r_symmetry_hbond_refined 0.572
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.822 r_dihedral_angle_4_deg 19.539 r_dihedral_angle_3_deg 18.38 r_scangle_it 14.419 r_scbond_it 11.706 r_dihedral_angle_1_deg 7.998 r_mcangle_it 7.691 r_mcbond_it 5.435 r_angle_refined_deg 1.706 r_symmetry_hbond_refined 0.572 r_nbd_refined 0.339 r_nbtor_refined 0.339 r_symmetry_vdw_refined 0.314 r_xyhbond_nbd_refined 0.275 r_xyhbond_nbd_other 0.227 r_chiral_restr 0.146 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_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 7236 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection HKL-2000 data reduction CNS phasing