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Crystal structure of Ompk36 GD at 3500 eV based on spherical harmonics 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 3.2 61.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 232.078 α = 90 b = 74.7 β = 112.209 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 2021-05-20 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 2.34 107.4 98.85 0.997 16.42 11 60662
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 2.42 0.896
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.34 107.4 60662 3261 98.758 0.205 0.2023 0.2023 0.2437 0.2437 41.487
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] 0.225 0.43 -2.735 1.619
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.873 r_dihedral_angle_3_deg 13.356 r_lrange_it 7.972 r_lrange_other 7.968 r_dihedral_angle_2_deg 7.285 r_dihedral_angle_1_deg 6.889 r_scangle_it 6.458 r_scangle_other 6.448 r_mcangle_it 4.902 r_mcangle_other 4.902
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.873 r_dihedral_angle_3_deg 13.356 r_lrange_it 7.972 r_lrange_other 7.968 r_dihedral_angle_2_deg 7.285 r_dihedral_angle_1_deg 6.889 r_scangle_it 6.458 r_scangle_other 6.448 r_mcangle_it 4.902 r_mcangle_other 4.902 r_scbond_it 4.242 r_scbond_other 4.235 r_mcbond_it 3.471 r_mcbond_other 3.47 r_angle_refined_deg 1.429 r_angle_other_deg 0.503 r_symmetry_xyhbond_nbd_refined 0.209 r_symmetry_nbd_other 0.201 r_nbtor_refined 0.185 r_nbd_other 0.184 r_nbd_refined 0.181 r_symmetry_nbd_refined 0.172 r_xyhbond_nbd_refined 0.158 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.065 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8099 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing