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Structure of a peptide:N-glycanase-Rad23 complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 sodium chloride, MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 6.7 81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.801 α = 90 b = 128.801 β = 90 c = 128.376 γ = 120
Symmetry Space Group P 31 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 93 CCD KODAK 2005-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 4A 1.0721 PAL/PLS 4A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.8 30 97.4 30868 30868 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 91
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2.8 20 28388 28388 1471 97.47 0.23737 0.23737 0.23572 0.2377 0.2701 0.2327 RANDOM 63.515
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] 3.34 1.67 3.34 -5.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.756 r_dihedral_angle_3_deg 24.366 r_dihedral_angle_4_deg 22.802 r_dihedral_angle_1_deg 7.14 r_rigid_bond_restr 4.222 r_sphericity_free 3.905 r_scbond_it 3.454 r_scangle_it 3.281 r_mcangle_it 1.891 r_sphericity_bonded 1.737
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.756 r_dihedral_angle_3_deg 24.366 r_dihedral_angle_4_deg 22.802 r_dihedral_angle_1_deg 7.14 r_rigid_bond_restr 4.222 r_sphericity_free 3.905 r_scbond_it 3.454 r_scangle_it 3.281 r_mcangle_it 1.891 r_sphericity_bonded 1.737 r_angle_refined_deg 1.644 r_mcbond_it 1.044 r_nbtor_refined 0.334 r_nbd_refined 0.279 r_symmetry_vdw_refined 0.219 r_xyhbond_nbd_refined 0.2 r_symmetry_hbond_refined 0.158 r_chiral_restr 0.124 r_bond_refined_d 0.015 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3121 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing