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Crystal structure of obelin following Ca2+ triggered bioluminescence suggests neutral coelenteramide as the primary excited state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SL7 PDB ENTRY 1SL7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 277 2% PEG 400, 2.0 M ammonium sulfate, 0.1 M HEPES-Na , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K, pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.95 58.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.26 α = 90 b = 64.26 β = 90 c = 63.049 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 200 CCD MARRESEARCH 2005-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.87 64.28 80.3 0.069 0.075 25 5.2 17133 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.86 1.93 17.3 0.26 0.26 1.66 1.4
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 (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 1SL7 1.93 28.74 17133 15977 844 86.71 0.1924 0.19043 0.1884 0.22997 0.1938 RANDOM 28.128
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.97 r_dihedral_angle_4_deg 21.043 r_dihedral_angle_3_deg 15.102 r_dihedral_angle_1_deg 5.545 r_scangle_it 4.243 r_scbond_it 2.681 r_mcangle_it 1.621 r_angle_refined_deg 1.461 r_mcbond_it 0.936 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.97 r_dihedral_angle_4_deg 21.043 r_dihedral_angle_3_deg 15.102 r_dihedral_angle_1_deg 5.545 r_scangle_it 4.243 r_scbond_it 2.681 r_mcangle_it 1.621 r_angle_refined_deg 1.461 r_mcbond_it 0.936 r_nbtor_refined 0.302 r_nbd_refined 0.218 r_symmetry_vdw_refined 0.202 r_symmetry_hbond_refined 0.195 r_xyhbond_nbd_refined 0.18 r_metal_ion_refined 0.162 r_chiral_restr 0.113 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 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_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 1529 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing