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Crystal structure of LMNADK1 from Listeria monocytogenes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I2C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 PEG400 15-20% w/v, KCitrate 50 mM, KCl 300 mM, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.26 45.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.959 α = 90 b = 75.088 β = 90 c = 118.49 γ = 90
Symmetry Space Group I 2 2 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 CCD ADSC QUANTUM 210 2006-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.9 28.2 87.5 0.06 0.063 20.2 5.9 22000 19663 29.25
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 1.9 1.99 51.6 0.489 2.5 3.9 1644
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 (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 PDB2I2C 1.9 28.2 22528 19066 589 87.22 0.18914 0.18914 0.18815 0.1906 0.22181 0.2213 RANDOM 27.827
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] -0.5 2.42 -1.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.533 r_dihedral_angle_4_deg 25.401 r_dihedral_angle_1_deg 21.375 r_dihedral_angle_3_deg 17.385 r_angle_other_deg 1.615 r_scangle_it 1.6 r_scbond_it 1.431 r_angle_refined_deg 1.43 r_mcangle_it 0.847 r_mcbond_it 0.692
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.533 r_dihedral_angle_4_deg 25.401 r_dihedral_angle_1_deg 21.375 r_dihedral_angle_3_deg 17.385 r_angle_other_deg 1.615 r_scangle_it 1.6 r_scbond_it 1.431 r_angle_refined_deg 1.43 r_mcangle_it 0.847 r_mcbond_it 0.692 r_symmetry_vdw_other 0.292 r_nbd_refined 0.217 r_nbd_other 0.212 r_symmetry_hbond_refined 0.185 r_nbtor_refined 0.178 r_symmetry_vdw_refined 0.16 r_xyhbond_nbd_refined 0.118 r_nbtor_other 0.098 r_mcbond_other 0.091 r_chiral_restr 0.089 r_bond_refined_d 0.01 r_bond_other_d 0.008 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2056 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling REFMAC phasing