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Crystal structure of the isolated MthK RCK domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LMQ PDB entry 1LMQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 0.1M Sodium cacodylate pH 6.5, 1.3-1.5M Lithium sulfate, 2% Benzamidine-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 4.24 71.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 165.89 α = 90 b = 165.89 β = 90 c = 82.22 γ = 120
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 ADSC QUANTUM 4 2005-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL1-5 0.97944 SSRL BL1-5
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3.2 30 91.7 0.068 21.5 6.4 7325 6717
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) 1 3.2 3.31 59.7 0.293 5.2 6.4 434
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1LMQ 3.23 30 6717 6416 300 95.32 0.23467 0.23182 0.2317 0.29937 0.2363 RANDOM 122.99
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] -6.81 -3.4 -6.81 10.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.863 r_dihedral_angle_3_deg 24.24 r_dihedral_angle_4_deg 20.087 r_dihedral_angle_1_deg 6.195 r_scangle_it 1.56 r_angle_refined_deg 1.355 r_mcangle_it 0.945 r_scbond_it 0.862 r_mcbond_it 0.528 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.863 r_dihedral_angle_3_deg 24.24 r_dihedral_angle_4_deg 20.087 r_dihedral_angle_1_deg 6.195 r_scangle_it 1.56 r_angle_refined_deg 1.355 r_mcangle_it 0.945 r_scbond_it 0.862 r_mcbond_it 0.528 r_nbtor_refined 0.314 r_symmetry_vdw_refined 0.272 r_nbd_refined 0.265 r_symmetry_hbond_refined 0.176 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 1719 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction SCALEPACK data scaling PHASER phasing