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Crystal structure of UNC119 in complex with Squarunkin A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6H6A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 30% w/v PEG3350
100 mM Sodium acetate pH 4.6
200-mM ammonium acetate
Crystal Properties Matthews coefficient Solvent content 2.61 52.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.73 α = 90 b = 80.63 β = 90 c = 191.03 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 PIXEL DECTRIS EIGER X 16M 2019-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.21 74.395 100 0.998 10.6 6.7 61768
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.21 2.27 0.626
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.21 74.395 61692 3200 99.947 0.224 0.2223 0.2574 0.2361 44.522
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] 1.396 1.474 -2.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.811 r_dihedral_angle_3_deg 15.297 r_lrange_it 8.651 r_lrange_other 8.648 r_dihedral_angle_1_deg 7.532 r_scangle_it 6.388 r_scangle_other 6.387 r_mcangle_it 5.258 r_mcangle_other 5.257 r_dihedral_angle_2_deg 4.977
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.811 r_dihedral_angle_3_deg 15.297 r_lrange_it 8.651 r_lrange_other 8.648 r_dihedral_angle_1_deg 7.532 r_scangle_it 6.388 r_scangle_other 6.387 r_mcangle_it 5.258 r_mcangle_other 5.257 r_dihedral_angle_2_deg 4.977 r_scbond_it 4.036 r_scbond_other 4.035 r_mcbond_it 3.537 r_mcbond_other 3.533 r_angle_refined_deg 0.727 r_angle_other_deg 0.289 r_symmetry_nbd_other 0.222 r_nbd_other 0.217 r_nbd_refined 0.199 r_nbtor_refined 0.188 r_xyhbond_nbd_refined 0.151 r_ncsr_local_group_5 0.126 r_ncsr_local_group_15 0.121 r_ncsr_local_group_14 0.113 r_ncsr_local_group_12 0.112 r_ncsr_local_group_9 0.11 r_ncsr_local_group_2 0.109 r_ncsr_local_group_3 0.106 r_ncsr_local_group_1 0.104 r_ncsr_local_group_8 0.104 r_ncsr_local_group_6 0.103 r_ncsr_local_group_11 0.103 r_ncsr_local_group_13 0.103 r_symmetry_nbd_refined 0.096 r_ncsr_local_group_10 0.093 r_ncsr_local_group_4 0.089 r_ncsr_local_group_7 0.088 r_symmetry_xyhbond_nbd_refined 0.085 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.045 r_symmetry_xyhbond_nbd_other 0.044 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8162 Nucleic Acid Atoms Solvent Atoms 336 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing