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Crystal structure of Ompk36 GD at 3500 eV based on a combination of spherical harmonics and analytical absorption corrections
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6RCK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 0.1M Lithium sulfate, 0.1M sodium citrate pH 5.6 and 12% PEG4000
Crystal Properties Matthews coefficient Solvent content 3.19 61.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 232.078 α = 90 b = 74.7 β = 112.21 c = 91.35 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 80 PIXEL DECTRIS PILATUS 12M 2021-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I23 3.54 Diamond I23
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.34 107.43 98.86 0.998 24.92 11 60652
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.34 2.424 0.878
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 2.34 107.43 57401 3261 98.77 0.19473 0.19262 0.2003 0.23277 0.2361 RANDOM 39.852
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] -0.28 0.15 -2.48 1.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.427 r_long_range_B_refined 8.084 r_long_range_B_other 8.075 r_dihedral_angle_2_deg 7.436 r_dihedral_angle_1_deg 6.854 r_scangle_other 6.632 r_mcangle_it 4.751 r_mcangle_other 4.751 r_scbond_it 4.359 r_scbond_other 4.352
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.427 r_long_range_B_refined 8.084 r_long_range_B_other 8.075 r_dihedral_angle_2_deg 7.436 r_dihedral_angle_1_deg 6.854 r_scangle_other 6.632 r_mcangle_it 4.751 r_mcangle_other 4.751 r_scbond_it 4.359 r_scbond_other 4.352 r_mcbond_it 3.372 r_mcbond_other 3.372 r_angle_refined_deg 1.45 r_angle_other_deg 0.512 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 8119 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing