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Crystal structure of DLC2 in complex with BMF peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XQQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Ammonium chloride 0.1 M HEPES 7.0 20 % w/v PEG 6000
Crystal Properties Matthews coefficient Solvent content 1.98 37.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 166.243 α = 90 b = 38.701 β = 99.87 c = 44.699 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 2017-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.98 SSRF BL18U1
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 41.93 98.98 0.997 11.78 5.6 19215
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 2.07 0.951
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 (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 2XQQ 2 41.93 17305 1923 99.27 0.19645 0.19325 0.2046 0.22565 0.2378 RANDOM 48.342
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] -1.74 1.42 3.19 -1.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.988 r_dihedral_angle_3_deg 15.574 r_dihedral_angle_4_deg 8.908 r_long_range_B_refined 8.389 r_long_range_B_other 8.38 r_scangle_other 6.603 r_dihedral_angle_1_deg 6.515 r_scbond_it 4.389 r_scbond_other 4.389 r_mcangle_it 3.472
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.988 r_dihedral_angle_3_deg 15.574 r_dihedral_angle_4_deg 8.908 r_long_range_B_refined 8.389 r_long_range_B_other 8.38 r_scangle_other 6.603 r_dihedral_angle_1_deg 6.515 r_scbond_it 4.389 r_scbond_other 4.389 r_mcangle_it 3.472 r_mcangle_other 3.438 r_mcbond_it 2.66 r_mcbond_other 2.631 r_angle_refined_deg 1.436 r_angle_other_deg 1.073 r_chiral_restr 0.095 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2158 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing