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Crystal structure of gluconate kinase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 277 PEG6000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.45 49.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.274 α = 90 b = 89.206 β = 105.14 c = 51.479 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH 2001-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B 0.845 EMBL/DESY, HAMBURG BW7B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.3 25 96.6 0.049 27.8 3 17024 17024 31.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.34 98.6 0.254 5.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.28 50 15607 15607 789 95.51 0.21665 0.21665 0.21356 0.2152 0.27657 0.2697 RANDOM 31.153
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] 2.3 1.13 0.26 -1.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.595 r_dihedral_angle_1_deg 3.735 r_scangle_it 3.241 r_scbond_it 1.933 r_angle_refined_deg 1.54 r_mcangle_it 1.295 r_mcbond_it 0.686 r_symmetry_vdw_refined 0.26 r_nbd_refined 0.253 r_symmetry_hbond_refined 0.217
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.595 r_dihedral_angle_1_deg 3.735 r_scangle_it 3.241 r_scbond_it 1.933 r_angle_refined_deg 1.54 r_mcangle_it 1.295 r_mcbond_it 0.686 r_symmetry_vdw_refined 0.26 r_nbd_refined 0.253 r_symmetry_hbond_refined 0.217 r_xyhbond_nbd_refined 0.18 r_chiral_restr 0.098 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_symmetry_vdw_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2702 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 64
Software Software Software Name Purpose AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling