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Crystal structure of monomeric KlHxk1 in crystal form XI with glucose bound (closed state)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3O08 PDB entry 3O08
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 292 0.2microL reservoir + 0.2microL protein, reservoir: 20% PEG6000, 1M LiCl, 0.1M Hepes pH 7.0, protein: 6.6mg/ml KlHxk1, 10mM Tris pH 7.4, 1mM EDTA, 1mM DTT, 0.5mM PMSF, 10mM AMPPNP, 10mM Glucose, 10mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.36 47.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.575 α = 90 b = 75.599 β = 90 c = 103.857 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 CCD MARMOSAIC 225 mm CCD 1st mirror: Silicon, active surface 50 nm Rh-coated, 2nd mirror: Glas, active surface 50 nm Rh-coated 2008-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2
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 1.42 30 96.2 0.05 22.6 7.1 96547 92838 -3 23.1
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) 1.42 1.46 72.7 0.491 2.9 4.1 5134
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB entry 3O08 1.42 29.7 91406 1367 96.19 0.18694 0.18651 0.2132 0.21578 0.2316 RANDOM 18.898
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] -0.35 -0.99 1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.218 r_dihedral_angle_4_deg 16.89 r_dihedral_angle_3_deg 12.534 r_dihedral_angle_1_deg 6.565 r_scangle_it 4.365 r_scbond_it 3.257 r_angle_refined_deg 2.313 r_mcangle_it 2.224 r_mcbond_it 1.679 r_chiral_restr 0.163
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.218 r_dihedral_angle_4_deg 16.89 r_dihedral_angle_3_deg 12.534 r_dihedral_angle_1_deg 6.565 r_scangle_it 4.365 r_scbond_it 3.257 r_angle_refined_deg 2.313 r_mcangle_it 2.224 r_mcbond_it 1.679 r_chiral_restr 0.163 r_bond_refined_d 0.028 r_gen_planes_refined 0.015 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3669 Nucleic Acid Atoms Solvent Atoms 611 Heterogen Atoms 28
Software Software Software Name Purpose MAR345 data collection AMoRE phasing REFMAC refinement XDS data reduction XSCALE data scaling