☰ Navigation Tabs
Structure of the 6-4 photolyase of D. melanogaster in complex with the non-natural N4-methyl T(Dewar)C lesion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CVU PDB ENTRY 3CVU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 291 100 MM HEPES, PH 7, 13-17% PEG1500, 18C
Crystal Properties Matthews coefficient Solvent content 2.95 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.169 α = 90 b = 87.486 β = 90 c = 91.856 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 CCD MARMOSAIC 225 mm CCD 2009-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA SLS X06DA
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 2.3 43.73 99.3 0.06 18.1 4 32351 2 42.4
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 2.3 2.42 99.7 0.4 3.9 4.1
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 3CVU 2.3 43.74 30688 1620 99.17 0.20265 0.20129 0.1975 0.22848 0.2288 RANDOM 27.233
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] 0.02 0.88 -0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.493 r_dihedral_angle_4_deg 15.619 r_dihedral_angle_3_deg 13.928 r_dihedral_angle_1_deg 4.998 r_scangle_it 4.127 r_scbond_it 2.685 r_mcangle_it 1.959 r_angle_refined_deg 1.22 r_mcbond_it 1.041 r_angle_other_deg 0.933
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.493 r_dihedral_angle_4_deg 15.619 r_dihedral_angle_3_deg 13.928 r_dihedral_angle_1_deg 4.998 r_scangle_it 4.127 r_scbond_it 2.685 r_mcangle_it 1.959 r_angle_refined_deg 1.22 r_mcbond_it 1.041 r_angle_other_deg 0.933 r_mcbond_other 0.221 r_chiral_restr 0.103 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.005 r_gen_planes_other 0.001 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_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 4162 Nucleic Acid Atoms 609 Solvent Atoms 170 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing