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Photoactive Yellow Protein PYP 10ps
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WL9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 SMALL TUBES 7 293 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 273 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 1.6 11.15 92.76 11.77 284.4 12253
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 1.6 1.64
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 4WL9 1.6 11.15 12253 613 92.76 0.28612 0.28335 0.2757 0.3415 0.3295 RANDOM 3.357
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] 0.02 0.01 0.02 -0.06
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 2.236 r_long_range_B_refined 1.155 r_angle_other_deg 1.043 r_long_range_B_other 0.868 r_mcangle_it 0.374 r_mcangle_other 0.374 r_mcbond_it 0.215 r_mcbond_other 0.215 r_scangle_other 0.193 r_chiral_restr 0.121
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 2.236 r_long_range_B_refined 1.155 r_angle_other_deg 1.043 r_long_range_B_other 0.868 r_mcangle_it 0.374 r_mcangle_other 0.374 r_mcbond_it 0.215 r_mcbond_other 0.215 r_scangle_other 0.193 r_chiral_restr 0.121 r_scbond_it 0.113 r_scbond_other 0.113 r_bond_refined_d 0.02 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