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Spore photoproduct lyase complexed with dinucleoside spore photoproduct
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FHC wt structure without substrate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 200 mM Li-sulfate, 100 mM Tris/HCl, 19-27% PEG800, 70 mM HEGA-8, anaerobically , pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.41 48.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.32 α = 90 b = 58.92 β = 90 c = 131.62 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 PSI PILATUS 6M 2011-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00000 SLS X10SA
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 71.93 99.6 0.071 28692 28692 -3 -3
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 2.1 99.7 0.484
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 (All) 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 wt structure without substrate 2 71.93 27252 27252 1440 99.63 0.22119 0.22119 0.21944 0.2013 0.25383 0.2403 RANDOM 27.514
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] 0.32 0.04 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.587 r_dihedral_angle_4_deg 14.847 r_dihedral_angle_3_deg 14.357 r_dihedral_angle_1_deg 5.751 r_scangle_it 2.659 r_scbond_it 1.566 r_angle_refined_deg 1.14 r_mcangle_it 1.137 r_angle_other_deg 0.833 r_mcbond_it 0.593
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.587 r_dihedral_angle_4_deg 14.847 r_dihedral_angle_3_deg 14.357 r_dihedral_angle_1_deg 5.751 r_scangle_it 2.659 r_scbond_it 1.566 r_angle_refined_deg 1.14 r_mcangle_it 1.137 r_angle_other_deg 0.833 r_mcbond_it 0.593 r_mcbond_other 0.104 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.002 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2802 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 103
Software Software Software Name Purpose HEIDI data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling