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Crystal structure of monomeric photosensitizing fluorescent protein, Supernova
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A8S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 293 0.1M SODIUM ACETATE, 2.2M SODIUM CHLORIDE, 0.2M LITHIUM SULFATE, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.16 43.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.252 α = 70.57 b = 89.304 β = 89.95 c = 109.885 γ = 71.62
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 2009-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A Photon Factory AR-NW12A
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 50 97.9 0.07 23.5 3.1 88149 -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 2.3 2.34 97.1 0.323 5.1 3.1
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 3A8S 2.3 20 83631 4432 97.5 0.184 0.181 0.1875 0.234 0.2346 RANDOM 28.1
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] 0.31 -0.86 0.55 0.52 -0.74 -1.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.286 r_dihedral_angle_4_deg 18.214 r_dihedral_angle_3_deg 16.921 r_dihedral_angle_1_deg 7.025 r_angle_refined_deg 1.942 r_angle_other_deg 0.856 r_chiral_restr 0.103 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.286 r_dihedral_angle_4_deg 18.214 r_dihedral_angle_3_deg 16.921 r_dihedral_angle_1_deg 7.025 r_angle_refined_deg 1.942 r_angle_other_deg 0.856 r_chiral_restr 0.103 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13795 Nucleic Acid Atoms Solvent Atoms 508 Heterogen Atoms
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling