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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 2.55 51.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.231 α = 90 b = 72.602 β = 90 c = 79.079 γ = 90
Symmetry Space Group P 21 21 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 IMAGE PLATE MARRESEARCH 2000-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 0.97830 EMBL/DESY, HAMBURG BW7A
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 2.6 25 99.3 0.063 27.9 12.6 13617 13617 30.9
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) 2.55 2.58 94.9 0.158 8.4
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 2.5 79.06 13603 13603 681 98.29 0.243 0.243 0.2399 0.2465 0.30421 0.3068 RANDOM 30.86
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] -1.76 3.55 -1.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.558 r_dihedral_angle_1_deg 4.103 r_scangle_it 4.041 r_scbond_it 2.428 r_angle_refined_deg 1.797 r_mcangle_it 1.695 r_mcbond_it 0.879 r_symmetry_hbond_refined 0.444 r_symmetry_vdw_refined 0.311 r_nbd_refined 0.276
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.558 r_dihedral_angle_1_deg 4.103 r_scangle_it 4.041 r_scbond_it 2.428 r_angle_refined_deg 1.797 r_mcangle_it 1.695 r_mcbond_it 0.879 r_symmetry_hbond_refined 0.444 r_symmetry_vdw_refined 0.311 r_nbd_refined 0.276 r_xyhbond_nbd_refined 0.164 r_chiral_restr 0.112 r_bond_refined_d 0.015 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 105 Heterogen Atoms 2
Software Software Software Name Purpose AMoRE phasing REFMAC refinement DENZO data reduction CCP4 data scaling