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Structure of the Gemin5 WD40 domain in complex with AAUUUUUGAG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OW8 3OW8,2HES,3DM0 experimental model PDB 2HES 3OW8,2HES,3DM0 experimental model PDB 3DM0 3OW8,2HES,3DM0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 0.1 M sodium citrate, 0.2 M ammonium acetate, 15% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.23 44.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.85 α = 90 b = 124.52 β = 116.77 c = 60.6 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS II 2016-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E DW 1.5418
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 1.85 28.92 99.9 0.998 14.9 7.3 65191
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 1.85 1.9 99.9 0.592 1.8 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 3OW8,2HES,3DM0 1.85 28.9 61867 3294 99.93 0.16614 0.16395 0.1752 0.20738 0.2125 RANDOM 24.115
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.108 r_dihedral_angle_4_deg 16.608 r_dihedral_angle_3_deg 12.916 r_dihedral_angle_1_deg 7.187 r_long_range_B_refined 6.239 r_long_range_B_other 6.163 r_scangle_other 4.308 r_mcangle_it 3.504 r_mcangle_other 3.504 r_scbond_it 2.943
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.108 r_dihedral_angle_4_deg 16.608 r_dihedral_angle_3_deg 12.916 r_dihedral_angle_1_deg 7.187 r_long_range_B_refined 6.239 r_long_range_B_other 6.163 r_scangle_other 4.308 r_mcangle_it 3.504 r_mcangle_other 3.504 r_scbond_it 2.943 r_scbond_other 2.942 r_mcbond_it 2.407 r_mcbond_other 2.402 r_angle_refined_deg 1.894 r_angle_other_deg 1.062 r_chiral_restr 0.119 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 5150 Nucleic Acid Atoms 82 Solvent Atoms 381 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALEPACK data scaling PHASER phasing