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crystal structure of oxidized hN33/Tusc3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4M8G pdb entry 4M8G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 0.2 M KSCN, 10.5% PEG
8K, 10% PEG 1K in 100 mM cacodylic acid-NaOH, pH 6.5, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.04 39.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.66 α = 90 b = 62.477 β = 90 c = 64.598 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 PIXEL DECTRIS PILATUS 6M 2009-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000 SLS X06SA
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 1.6 64 99.5 0.063 12.5 3.9 21247 21141 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.7 99.6 0.637 0.593 2.4 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 pdb entry 4M8G 1.6 32.32 20596 20596 443 98.88 0.18552 0.18484 0.2068 0.22003 0.2303 RANDOM 17.756
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] 0.33 0.19 -0.52
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_2_deg 31.858 f_dihedral_angle_4_deg 19.122 f_dihedral_angle_3_deg 12.835 f_long_range_B_other 10.63 f_long_range_B_refined 10.626 f_dihedral_angle_1_deg 6.508 f_scangle_other 5.868 f_mcangle_other 5.258 f_mcangle_it 5.255 f_scbond_it 3.578
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_2_deg 31.858 f_dihedral_angle_4_deg 19.122 f_dihedral_angle_3_deg 12.835 f_long_range_B_other 10.63 f_long_range_B_refined 10.626 f_dihedral_angle_1_deg 6.508 f_scangle_other 5.868 f_mcangle_other 5.258 f_mcangle_it 5.255 f_scbond_it 3.578 f_scbond_other 3.575 f_mcbond_it 3.094 f_mcbond_other 3.061 f_angle_refined_deg 1.781 f_angle_other_deg 0.891 f_chiral_restr 0.118 f_bond_refined_d 0.021 f_gen_planes_refined 0.009 f_bond_other_d 0.002 f_gen_planes_other 0.001 f_nbd_refined f_nbd_other f_nbtor_refined f_nbtor_other f_xyhbond_nbd_refined f_xyhbond_nbd_other f_metal_ion_refined f_metal_ion_other f_symmetry_vdw_refined f_symmetry_vdw_other f_symmetry_hbond_refined f_symmetry_hbond_other f_symmetry_metal_ion_refined f_symmetry_metal_ion_other f_scangle_it f_rigid_bond_restr f_sphericity_free f_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1263 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms
Software Software Software Name Purpose PHASER phasing PHENIX refinement REFMAC refinement XDS data reduction SCALA data scaling