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Crystal structure of unliganded MYORG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F2H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 100 mM HEPES pH 7.0, 10% PEG MME5000 and 5% tasimate pH 7.0.
Crystal Properties Matthews coefficient Solvent content 3.16 61.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.109 α = 88.062 b = 78.986 β = 78.801 c = 180.113 γ = 62.714
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 XE 16M 2019-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97951 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.43 66.57 98.2 0.066 0.093 0.066 0.983 8.2 2.2 131515
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.43 2.47 1.071 1.514 1.071 0.515 1 2.1
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2F2H 2.43 66.57 131476 6445 98.149 0.212 0.2108 0.233 0.2278 58.353
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] -0.158 0.096 -1.604 1.904 0.501 -3.268
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.627 r_dihedral_angle_4_deg 17.561 r_dihedral_angle_3_deg 16.065 r_dihedral_angle_1_deg 7.035 r_lrange_it 3.972 r_lrange_other 3.966 r_scangle_it 1.54 r_scangle_other 1.54 r_mcangle_it 1.53 r_mcangle_other 1.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.627 r_dihedral_angle_4_deg 17.561 r_dihedral_angle_3_deg 16.065 r_dihedral_angle_1_deg 7.035 r_lrange_it 3.972 r_lrange_other 3.966 r_scangle_it 1.54 r_scangle_other 1.54 r_mcangle_it 1.53 r_mcangle_other 1.53 r_angle_refined_deg 1.377 r_angle_other_deg 1.139 r_mcbond_it 0.908 r_mcbond_other 0.908 r_scbond_it 0.908 r_scbond_other 0.908 r_nbd_other 0.245 r_nbd_refined 0.184 r_symmetry_xyhbond_nbd_refined 0.177 r_symmetry_nbd_other 0.176 r_nbtor_refined 0.164 r_symmetry_nbd_refined 0.151 r_xyhbond_nbd_refined 0.142 r_ncsr_local_group_3 0.092 r_ncsr_local_group_5 0.092 r_ncsr_local_group_6 0.085 r_ncsr_local_group_4 0.078 r_ncsr_local_group_2 0.077 r_ncsr_local_group_1 0.076 r_symmetry_nbtor_other 0.072 r_chiral_restr 0.055 r_symmetry_xyhbond_nbd_other 0.046 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19386 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms 531
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing