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Crystal Structure of LHK-Exo in complex with dAMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SYY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.4 293 0.1M Tris pH 8.4, 1.0M potassium sodium tartrate tetrahydrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.31 62.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.327 α = 90 b = 108.327 β = 90 c = 47.824 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 IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2009-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 2.59 50 99.5 0.047 43.7 4.5 10125 10072 -3
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 2.6 2.64 100 0.473 4.3 4.5 509
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3SYY 2.59 50 9636 9575 487 99.36 0.21044 0.20791 0.26215 0.2663 RANDOM 65.594
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] 1.05 0.53 1.05 -1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.433 r_dihedral_angle_3_deg 17.995 r_dihedral_angle_4_deg 15.003 r_dihedral_angle_1_deg 6.146 r_scangle_it 3.143 r_scbond_it 1.808 r_angle_refined_deg 1.608 r_mcangle_it 1.429 r_mcbond_it 0.76 r_chiral_restr 0.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.433 r_dihedral_angle_3_deg 17.995 r_dihedral_angle_4_deg 15.003 r_dihedral_angle_1_deg 6.146 r_scangle_it 3.143 r_scbond_it 1.808 r_angle_refined_deg 1.608 r_mcangle_it 1.429 r_mcbond_it 0.76 r_chiral_restr 0.097 r_bond_refined_d 0.016 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1529 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 23
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling