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Crystal structure of the EndoG/EndoGI complex: Mechanism of EndoG inhibition
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O3B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 20%(w/v)PEG 2000 MME, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.3 46.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.79 α = 90 b = 109.15 β = 90 c = 121.08 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 CCD MARMOSAIC 225 mm CCD 2009-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0075 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 43.23 95.9 0.184 14.8 4.1 46364 46364 38
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.3 90.5 0.201 4.2 4.2 5385
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 2O3B 2.2 43.23 45828 2412 100 0.1864 0.18444 0.1866 0.22308 0.224 RANDOM 31.796
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] -0.91 0.37 0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.428 r_dihedral_angle_4_deg 18.608 r_dihedral_angle_3_deg 14.109 r_dihedral_angle_1_deg 5.896 r_scangle_it 2.03 r_scbond_it 1.378 r_angle_refined_deg 1.15 r_mcangle_it 0.878 r_mcbond_it 0.533 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.428 r_dihedral_angle_4_deg 18.608 r_dihedral_angle_3_deg 14.109 r_dihedral_angle_1_deg 5.896 r_scangle_it 2.03 r_scbond_it 1.378 r_angle_refined_deg 1.15 r_mcangle_it 0.878 r_mcbond_it 0.533 r_nbtor_refined 0.304 r_symmetry_hbond_refined 0.236 r_nbd_refined 0.179 r_xyhbond_nbd_refined 0.167 r_symmetry_vdw_refined 0.15 r_chiral_restr 0.086 r_metal_ion_refined 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6299 Nucleic Acid Atoms Solvent Atoms 328 Heterogen Atoms 10
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XDS data scaling