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Crystal structure of the cryorhodopsin CryoR2 at pH 4.6, type B crystals, illuminated state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other model from cryo-EM data
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 4.6 293 1.2M Na/K-Pi pH 4.6
Crystal Properties Matthews coefficient Solvent content 2.67 53.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.108 α = 90 b = 84.964 β = 96.87 c = 296.943 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS EIGER2 X 16M 2023-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9763 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) CC (Half) 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 2.774 74.387 63.34 0.085 0.9987 6.512 6.88 59820
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.774 3.1 1.061 0.3825
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3 20 54950 2850 77.2 0.28814 0.28701 0.30938 0.2582 RANDOM 84.75
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] 1.9 -0.08 0.95 -2.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.35 r_dihedral_angle_3_deg 9.979 r_scangle_other 8.941 r_mcangle_it 8.871 r_mcangle_other 8.871 r_dihedral_angle_4_deg 8.489 r_mcbond_it 5.485 r_mcbond_other 5.484 r_scbond_it 5.435 r_scbond_other 5.427
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.35 r_dihedral_angle_3_deg 9.979 r_scangle_other 8.941 r_mcangle_it 8.871 r_mcangle_other 8.871 r_dihedral_angle_4_deg 8.489 r_mcbond_it 5.485 r_mcbond_other 5.484 r_scbond_it 5.435 r_scbond_other 5.427 r_dihedral_angle_1_deg 2.658 r_angle_other_deg 1.137 r_angle_refined_deg 1.07 r_chiral_restr 0.032 r_bond_other_d 0.004 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_gen_planes_other 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21522 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 326
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling MOLREP phasing