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Crystal Structure of ETD97N-EHred complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A8J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 288 14.4% PEG8000, 0.036M KH2PO4, 18% Glycerol, 0.05M NaCl, 1mM CTAB, 1mM MgCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.42 49.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.122 α = 91.56 b = 88.412 β = 102.42 c = 97.863 γ = 89.59
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 Bruker DIP-6040 2008-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9000 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.95 50 98.3 0.071 20.9 4 119927
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) 1 1.95 1.98 0.442 3.2 3.9
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 3A8J 1.95 43.97 119927 6363 98.09 0.1739 0.17094 0.1714 0.22915 0.2284 RANDOM 25.512
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] 0.05 0.21 -0.87 -0.52 -0.06 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.079 r_dihedral_angle_4_deg 17.138 r_dihedral_angle_3_deg 15.331 r_dihedral_angle_1_deg 6.608 r_scangle_it 5.017 r_scbond_it 3.221 r_mcangle_it 1.971 r_angle_refined_deg 1.867 r_mcbond_it 1.192 r_chiral_restr 0.141
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.079 r_dihedral_angle_4_deg 17.138 r_dihedral_angle_3_deg 15.331 r_dihedral_angle_1_deg 6.608 r_scangle_it 5.017 r_scbond_it 3.221 r_mcangle_it 1.971 r_angle_refined_deg 1.867 r_mcbond_it 1.192 r_chiral_restr 0.141 r_bond_refined_d 0.023 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13164 Nucleic Acid Atoms Solvent Atoms 1495 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling