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Crystal structure of Ragulator
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VET 1VET, 3MS6 experimental model PDB 3MS6 1VET, 3MS6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292 0.1 M CHES pH 9.0, 40% PEG 600
Crystal Properties Matthews coefficient Solvent content 2.91 57.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.705 α = 90 b = 168.705 β = 90 c = 52.325 γ = 120
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 PILATUS3 S 6M 2017-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.12 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.425 146.103 93.6 12.12 9.1 271960
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 1VET, 3MS6 1.42 146.1 135926 1860 86.77 0.21196 0.21163 0.2179 0.23703 0.2459 RANDOM 32.526
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] 0.09 0.04 0.09 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.603 r_dihedral_angle_4_deg 14.641 r_dihedral_angle_3_deg 12.555 r_dihedral_angle_1_deg 5.383 r_long_range_B_refined 4.757 r_long_range_B_other 4.721 r_scangle_other 4.042 r_angle_other_deg 3.581 r_scbond_it 2.782 r_scbond_other 2.782
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.603 r_dihedral_angle_4_deg 14.641 r_dihedral_angle_3_deg 12.555 r_dihedral_angle_1_deg 5.383 r_long_range_B_refined 4.757 r_long_range_B_other 4.721 r_scangle_other 4.042 r_angle_other_deg 3.581 r_scbond_it 2.782 r_scbond_other 2.782 r_mcangle_it 2.626 r_mcangle_other 2.626 r_mcbond_it 1.887 r_mcbond_other 1.887 r_angle_refined_deg 1.365 r_chiral_restr 0.081 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_gen_planes_other 0.003 r_bond_other_d 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 3707 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHASER phasing Coot model building XDS data reduction XDS data scaling