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Frog EPDR1 with an Ir atom
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6JL9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.2M Calcium acetate hydrate, 0.1M Sodium cacodylate trihydrate pH 6.5, 10-25% w/v Polyethylene glycol 8000
Crystal Properties Matthews coefficient Solvent content 2.99 58.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.008 α = 90 b = 62.008 β = 90 c = 233.409 γ = 120
Symmetry Space Group P 65 2 2
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 2018-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 1.1054 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.4 53.7 98.3 0.078 0.997 79.3 18.2 11076
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.44 0.363 0.991 17.7
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 6JL9 2.4 35.26 10455 526 98.05 0.23629 0.23344 0.2381 0.29333 0.2932 RANDOM 50.342
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] 1.08 0.54 1.08 -3.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.269 r_dihedral_angle_4_deg 20.128 r_dihedral_angle_3_deg 18.704 r_long_range_B_other 11.33 r_long_range_B_refined 11.326 r_dihedral_angle_1_deg 9.505 r_scangle_other 8.169 r_mcangle_other 6.769 r_mcangle_it 6.765 r_scbond_it 5.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.269 r_dihedral_angle_4_deg 20.128 r_dihedral_angle_3_deg 18.704 r_long_range_B_other 11.33 r_long_range_B_refined 11.326 r_dihedral_angle_1_deg 9.505 r_scangle_other 8.169 r_mcangle_other 6.769 r_mcangle_it 6.765 r_scbond_it 5.27 r_scbond_other 5.269 r_mcbond_it 4.596 r_mcbond_other 4.585 r_angle_refined_deg 1.659 r_angle_other_deg 1.216 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 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 1524 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing