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Crystal structure of Ld-HF10
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LD9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 277 20% w/v PEG10K, 0.1M Sodium citrate tribasic dihydrate pH5.5, and 1M Lithium sulfate monohydrate
Crystal Properties Matthews coefficient Solvent content 3.05 59.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.503 α = 90 b = 139.816 β = 130.824 c = 87.344 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 S 6M 2016-08-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.979 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 1.8 77 99.6 0.05 9.6 3.4 102152 31.23
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 1.8 1.864 0.738
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1LD9 1.8 50.005 100636 5081 98.798 0.18 0.1777 0.1858 0.2186 0.223 39.482
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] -0.458 0.343 -0.981 0.339
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.47 r_dihedral_angle_4_deg 18.826 r_dihedral_angle_3_deg 16.391 r_lrange_it 8.345 r_lrange_other 8.345 r_dihedral_angle_1_deg 7.594 r_scangle_it 6.564 r_scangle_other 6.564 r_scbond_it 4.375 r_scbond_other 4.375
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.47 r_dihedral_angle_4_deg 18.826 r_dihedral_angle_3_deg 16.391 r_lrange_it 8.345 r_lrange_other 8.345 r_dihedral_angle_1_deg 7.594 r_scangle_it 6.564 r_scangle_other 6.564 r_scbond_it 4.375 r_scbond_other 4.375 r_mcangle_it 4.215 r_mcangle_other 4.215 r_mcbond_it 3.047 r_mcbond_other 3.046 r_angle_refined_deg 2.08 r_angle_other_deg 1.542 r_symmetry_nbd_refined 0.302 r_nbd_refined 0.217 r_symmetry_nbd_other 0.203 r_nbd_other 0.186 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.164 r_symmetry_xyhbond_nbd_refined 0.159 r_chiral_restr 0.099 r_symmetry_nbtor_other 0.091 r_symmetry_xyhbond_nbd_other 0.038 r_bond_refined_d 0.017 r_gen_planes_refined 0.014 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6240 Nucleic Acid Atoms Solvent Atoms 401 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing