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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 2.39 48.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.74 α = 90 b = 88.41 β = 105.76 c = 51.48 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 CCD BRUKER SMART 1000 2001-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 1.093 MAX II I711
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 2.8 49.39 99.7 0.11 4.5 4.1 9047 9047 58.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.8 2.95 99.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 2.8 25 10542 575 97.88 0.25471 0.25166 0.2375 0.31472 0.2944 RANDOM 58.105
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] 5.09 2.52 1.97 -5.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.527 r_dihedral_angle_1_deg 4.349 r_scangle_it 3.775 r_scbond_it 2.433 r_angle_refined_deg 2.164 r_mcangle_it 1.504 r_mcbond_it 0.835 r_symmetry_hbond_refined 0.586 r_symmetry_vdw_refined 0.526 r_nbd_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.527 r_dihedral_angle_1_deg 4.349 r_scangle_it 3.775 r_scbond_it 2.433 r_angle_refined_deg 2.164 r_mcangle_it 1.504 r_mcbond_it 0.835 r_symmetry_hbond_refined 0.586 r_symmetry_vdw_refined 0.526 r_nbd_refined 0.299 r_xyhbond_nbd_refined 0.259 r_chiral_restr 0.12 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 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 r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2694 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 64
Software Software Software Name Purpose AMoRE phasing REFMAC refinement MOSFLM data reduction CCP4 data scaling