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Crystal structure of gluconate kinase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 PEG 6000, LiCl, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.55 51.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.556 α = 90 b = 79.167 β = 105.2 c = 70.091 γ = 90
Symmetry Space Group C 1 2 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 1998-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 1.282 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 2.1 67.42 97.9 0.06 19.6 3.4 22646 22646 33.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.14 76.1 0.192 3.9
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 2.09 25 21544 1102 97.13 0.22092 0.21785 0.2203 0.27965 0.2767 RANDOM 33.792
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] 2.77 0.7 -1.48 -0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.546 r_scangle_it 3.579 r_dihedral_angle_1_deg 3.469 r_scbond_it 2.201 r_mcangle_it 1.684 r_symmetry_hbond_refined 1.555 r_angle_refined_deg 1.43 r_mcbond_it 0.903 r_symmetry_vdw_refined 0.561 r_nbd_refined 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.546 r_scangle_it 3.579 r_dihedral_angle_1_deg 3.469 r_scbond_it 2.201 r_mcangle_it 1.684 r_symmetry_hbond_refined 1.555 r_angle_refined_deg 1.43 r_mcbond_it 0.903 r_symmetry_vdw_refined 0.561 r_nbd_refined 0.26 r_xyhbond_nbd_refined 0.21 r_chiral_restr 0.1 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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 2563 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 2
Software Software Software Name Purpose AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling