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Thermus DNA photolyase with 8-Iod-riboflavin antenna chromophore
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IQR PDB ENTRY 1IQR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 50 MM TRIS-HCL, PH 8.5, 1.0 M NH4H2PO4, 11.8 MG/ML PROTEIN. CRYSTAL WAS SOAKED WITH 0.1 MM FMN FOR 90 MIN PRIOR TO FREEZING.
Crystal Properties Matthews coefficient Solvent content 2.57 51.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.62 α = 90 b = 112.62 β = 90 c = 140.262 γ = 120
Symmetry Space Group P 61 2 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 IMAGE PLATE MARRESEARCH OSMIC MIRRORS 2003-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591
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 2.6 24.4 91.5 0.14 10.9 2.2 19019 -3
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 1IQR 2.61 24.32 14393 771 91.6 0.167 0.163 0.1631 0.256 0.2537 RANDOM 26.44
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] 0.09 0.04 0.09 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.321 r_dihedral_angle_4_deg 21.861 r_dihedral_angle_3_deg 21.169 r_dihedral_angle_1_deg 9.06 r_scangle_it 8.629 r_scbond_it 6.521 r_mcangle_it 3.897 r_mcbond_it 2.621 r_angle_refined_deg 2.281 r_nbtor_refined 0.334
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.321 r_dihedral_angle_4_deg 21.861 r_dihedral_angle_3_deg 21.169 r_dihedral_angle_1_deg 9.06 r_scangle_it 8.629 r_scbond_it 6.521 r_mcangle_it 3.897 r_mcbond_it 2.621 r_angle_refined_deg 2.281 r_nbtor_refined 0.334 r_symmetry_vdw_refined 0.279 r_nbd_refined 0.264 r_xyhbond_nbd_refined 0.216 r_chiral_restr 0.191 r_symmetry_hbond_refined 0.142 r_gen_planes_refined 0.026 r_bond_refined_d 0.025 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3372 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing