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Photoactive Yellow Protein PYP Pure Dark
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 SMALL TUBES 293 Sodium Malonate
Crystal Properties Matthews coefficient Solvent content 1.88 34.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.9 α = 90 b = 66.9 β = 90 c = 40.8 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 300 PIXEL AGIPD 2019-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER EUROPEAN XFEL BEAMLINE SPB/SFX 1.3 European XFEL SPB/SFX
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 1.7 11.15 94.32 5.06 57.6 10361
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.743
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.7 11.15 10361 573 94.32 0.17915 0.17568 0.1875 0.24143 0.2433 RANDOM 13.884
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] -0.13 -0.07 -0.13 0.44
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 6.451 r_long_range_B_other 6.099 r_scangle_other 3.696 r_mcangle_it 2.412 r_mcangle_other 2.412 r_scbond_it 2.311 r_scbond_other 2.311 r_angle_refined_deg 1.861 r_mcbond_it 1.535 r_mcbond_other 1.535
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 6.451 r_long_range_B_other 6.099 r_scangle_other 3.696 r_mcangle_it 2.412 r_mcangle_other 2.412 r_scbond_it 2.311 r_scbond_other 2.311 r_angle_refined_deg 1.861 r_mcbond_it 1.535 r_mcbond_other 1.535 r_angle_other_deg 0.961 r_chiral_restr 0.137 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 987 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling PHENIX phasing