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Crystal structure of DBJA (HIS-DBJA)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BN6 PDB ENTRY 1BN6
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 2.5 50.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 212.855 α = 90 b = 117.843 β = 90 c = 55.796 γ = 90
Symmetry Space Group P 21 21 2
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 2005-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 0.98 Photon Factory BL-5A
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 1.75 50 95.2 0.041 6.1 134673
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) 1.75 1.81 90.7 0.175 5.6
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 1BN6 1.75 35.18 127902 6770 95.09 0.16794 0.16674 0.1721 0.19076 0.1948 RANDOM 19.867
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] -0.13 0.07 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.605 r_dihedral_angle_4_deg 19.028 r_dihedral_angle_3_deg 12.553 r_dihedral_angle_1_deg 5.184 r_scangle_it 3.366 r_scbond_it 2 r_angle_refined_deg 1.275 r_mcangle_it 1.233 r_mcbond_it 0.654 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.605 r_dihedral_angle_4_deg 19.028 r_dihedral_angle_3_deg 12.553 r_dihedral_angle_1_deg 5.184 r_scangle_it 3.366 r_scbond_it 2 r_angle_refined_deg 1.275 r_mcangle_it 1.233 r_mcbond_it 0.654 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.272 r_nbd_refined 0.2 r_xyhbond_nbd_refined 0.113 r_chiral_restr 0.089 r_symmetry_hbond_refined 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 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 9401 Nucleic Acid Atoms Solvent Atoms 1120 Heterogen Atoms 4
Software Software Software Name Purpose HKL-2000 data collection CNS refinement REFMAC refinement HKL-2000 data reduction DENZO data reduction SCALEPACK data scaling CNS phasing