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Crystal structure of gluconate kinase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 PEG6000, LiCl, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.36 47.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.951 α = 90 b = 79.294 β = 90 c = 89.703 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 100 IMAGE PLATE MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 0.995 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 25 99.8 0.054 12.6 5.3 25758 25758 22.8
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) 2 2.03 98.4 0.271 0.271 4.4
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 MOLECULAR REPLACEMENT THROUGHOUT 2 59.8 24469 1240 99.6 0.21129 0.20896 0.2134 0.25718 0.2604 RANDOM 22.763
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] -1.57 -0.25 1.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.617 r_dihedral_angle_1_deg 3.365 r_scangle_it 3.173 r_scbond_it 1.941 r_mcangle_it 1.311 r_angle_refined_deg 1.226 r_gen_planes_other 0.731 r_mcbond_it 0.704 r_symmetry_hbond_refined 0.448 r_nbd_refined 0.262
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.617 r_dihedral_angle_1_deg 3.365 r_scangle_it 3.173 r_scbond_it 1.941 r_mcangle_it 1.311 r_angle_refined_deg 1.226 r_gen_planes_other 0.731 r_mcbond_it 0.704 r_symmetry_hbond_refined 0.448 r_nbd_refined 0.262 r_xyhbond_nbd_refined 0.248 r_symmetry_vdw_refined 0.161 r_chiral_restr 0.085 r_gen_planes_refined 0.026 r_bond_refined_d 0.01 r_bond_other_d r_angle_other_deg 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 2695 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms 3
Software Software Software Name Purpose AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling