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Structure of a peptide:N-glycanase-Rad23 complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 291 sodium chloride, MES, pH 6, VAPOR DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 6.7 81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.235 α = 90 b = 129.235 β = 90 c = 128.494 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 0.9794 Photon Factory BL-5A
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 3 50 94.4 25391 25391 1 1
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) 3 3.1 68.9 0.32
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 SAD THROUGHOUT 3 20 22672 22672 1180 94.79 0.24516 0.24516 0.24367 0.2509 0.27418 0.2443 RANDOM 75.596
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] 5.4 2.7 5.4 -8.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.459 r_dihedral_angle_3_deg 23.857 r_dihedral_angle_4_deg 20.629 r_dihedral_angle_1_deg 7.129 r_rigid_bond_restr 5.017 r_sphericity_free 4.378 r_scbond_it 3.953 r_scangle_it 3.435 r_sphericity_bonded 1.945 r_mcangle_it 1.939
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.459 r_dihedral_angle_3_deg 23.857 r_dihedral_angle_4_deg 20.629 r_dihedral_angle_1_deg 7.129 r_rigid_bond_restr 5.017 r_sphericity_free 4.378 r_scbond_it 3.953 r_scangle_it 3.435 r_sphericity_bonded 1.945 r_mcangle_it 1.939 r_angle_refined_deg 1.688 r_mcbond_it 1.069 r_nbtor_refined 0.343 r_nbd_refined 0.296 r_xyhbond_nbd_refined 0.199 r_symmetry_vdw_refined 0.183 r_chiral_restr 0.117 r_symmetry_hbond_refined 0.078 r_bond_refined_d 0.015 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3100 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing