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1.7 Angstrom Crystal Structure of the Photo-excited Blue-light Photoreceptor Vivid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PD7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 30% PEG 5000 MME, 0.1M tri-sodium citrate, 0.1M ammonium acetate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.43 49.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.97 α = 90 b = 81.13 β = 89.94 c = 64.73 γ = 90
Symmetry Space Group P 1 21 1
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 315 2006-03-13 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315 2006-03-13 M SINGLE WAVELENGTH 3 1 x-ray 100 CCD ADSC QUANTUM 315 2006-03-13 M SINGLE WAVELENGTH 4 1 x-ray 100 CCD ADSC QUANTUM 315 2006-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.10 NSLS X29A 2 SYNCHROTRON NSLS BEAMLINE X29A 1.10 NSLS X29A 3 SYNCHROTRON NSLS BEAMLINE X29A 1.10 NSLS X29A 4 SYNCHROTRON NSLS BEAMLINE X29A 1.10 NSLS X29A
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 1,2,3,4 1.7 30 82.9 0.102 13.31 2.1 59234 59234 18.3
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) 1.7 1.76 63.6 0.431 1.91 1.8 4525
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 2PD7 1.7 30 59190 59190 6000 82.7 0.23 0.23 0.226 0.2338 0.249 0.256 Random
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]
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 2.206 c_scbond_it 1.507 c_mcangle_it 1.465 c_mcbond_it 0.919 c_bond_d c_angle_deg c_dihedral_angle_d c_improper_angle_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4988 Nucleic Acid Atoms Solvent Atoms 500 Heterogen Atoms 424
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing CNS refinement HKL-2000 data reduction SCALEPACK data scaling