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CRYSTAL STRUCTURE OF a putative 5-dehydro-2-deoxygluconokinase (IOLC) FROM BACILLUS HALODURANS C-125 AT 1.90 A RESOLUTION
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 NANODROP, 0.2M MgCl2, 50.0% PEG 200, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.53 65.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 194.001 α = 90 b = 194.001 β = 90 c = 48.083 γ = 120
Symmetry Space Group P 64 2 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 MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2007-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97901 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 1.9 29.161 100 0.093 0.093 4.8 10.4 42457
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 1.9 1.95 99.8 0.671 0.671 1 7.2 3074
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.9 29.161 42439 2143 99.97 0.176 0.175 0.196 0.2132 RANDOM 26.102
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] -0.5 -0.25 -0.5 0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.727 r_dihedral_angle_4_deg 17.047 r_dihedral_angle_3_deg 13.232 r_scangle_it 7.413 r_dihedral_angle_1_deg 5.975 r_scbond_it 5.64 r_mcangle_it 2.946 r_mcbond_it 2.21 r_angle_refined_deg 1.543 r_angle_other_deg 1.037
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.727 r_dihedral_angle_4_deg 17.047 r_dihedral_angle_3_deg 13.232 r_scangle_it 7.413 r_dihedral_angle_1_deg 5.975 r_scbond_it 5.64 r_mcangle_it 2.946 r_mcbond_it 2.21 r_angle_refined_deg 1.543 r_angle_other_deg 1.037 r_mcbond_other 0.544 r_symmetry_vdw_other 0.239 r_nbd_refined 0.221 r_symmetry_hbond_refined 0.214 r_symmetry_vdw_refined 0.212 r_nbd_other 0.197 r_chiral_restr 0.184 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.141 r_nbtor_other 0.085 r_bond_refined_d 0.016 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 2509 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SOLVE phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction