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Crystal structure of a single mutant of Dronpa, the green-on-state PDM1-4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z1O PDB entry 2z1o
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 289 25% PEG 3350, 0.1M Hepes pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.82 32.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.539 α = 90 b = 103.804 β = 90 c = 177.255 γ = 90
Symmetry Space Group P 2 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 2011-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.000 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.95 54.93 100 75756 75756
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.21 100 0.518 4 7.4
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB entry 2z1o 1.95 54.709 1.33 75756 94192 4728 99.95 0.186 0.1835 0.1802 0.2324 0.2267
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] 3.4672 4.0512 -7.5184
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.38 f_angle_d 1.303 f_chiral_restr 0.097 f_bond_d 0.009 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10337 Nucleic Acid Atoms Solvent Atoms 884 Heterogen Atoms 125
Software Software Software Name Purpose XDS data scaling PHASES phasing PHENIX refinement XDS data reduction SCALA data scaling