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Crystal structure of DBJA (mutant dbja delta)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A1O PDB ENTRY 3A1O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.9 293 PEG 4000, PH 7.9, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 2.37 48.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.547 α = 90 b = 48.652 β = 97.39 c = 106.816 γ = 90
Symmetry Space Group C 1 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 100 CCD ADSC QUANTUM 210 2005-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 0.978 Photon Factory AR-NW12A
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 1.78 50 98.6 0.072 10.8 3.5 60942
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) 1.78 1.84 92.4 0.349 2.7
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 PDB ENTRY 3A1O 1.78 43.19 57853 3088 98.8 0.171 0.169 0.1695 0.205 0.206 RANDOM 20.23
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.86 r_dihedral_angle_4_deg 19.29 r_dihedral_angle_3_deg 13.41 r_dihedral_angle_1_deg 5.145 r_scangle_it 3.843 r_scbond_it 2.33 r_mcangle_it 1.421 r_angle_refined_deg 1.403 r_mcbond_it 0.885 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.86 r_dihedral_angle_4_deg 19.29 r_dihedral_angle_3_deg 13.41 r_dihedral_angle_1_deg 5.145 r_scangle_it 3.843 r_scbond_it 2.33 r_mcangle_it 1.421 r_angle_refined_deg 1.403 r_mcbond_it 0.885 r_nbtor_refined 0.311 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.191 r_symmetry_hbond_refined 0.136 r_xyhbond_nbd_refined 0.118 r_chiral_restr 0.098 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 4543 Nucleic Acid Atoms Solvent Atoms 379 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction DENZO data reduction SCALEPACK data scaling