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Crystal structure of a Novel Tudor domain-containing protein SGF29
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ME9 PDB ENTRY 3ME9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 291 0.1M Sodium citrate tribasic dihydrate pH 5.6, 0.2M potassium sodium tartrate, 2M Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.93 36.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.802 α = 90 b = 51.29 β = 117.48 c = 44.842 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 100 CCD ADSC QUANTUM 210 2009-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.97800 CHESS A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.77 50 91.1 0.071 0.071 12.5 3.3 13275
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.77 1.8 59.5 0.301 2 427
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3ME9 1.78 25.09 12587 667 91.17 0.20848 0.20647 0.2451 0.2377 RANDOM 23.679
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] -0.19 -0.04 0.22 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.82 r_dihedral_angle_4_deg 25.132 r_dihedral_angle_3_deg 13.647 r_dihedral_angle_1_deg 7.207 r_scangle_it 4.253 r_scbond_it 2.558 r_mcangle_it 1.649 r_angle_refined_deg 1.394 r_mcbond_it 0.897 r_angle_other_deg 0.881
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.82 r_dihedral_angle_4_deg 25.132 r_dihedral_angle_3_deg 13.647 r_dihedral_angle_1_deg 7.207 r_scangle_it 4.253 r_scbond_it 2.558 r_mcangle_it 1.649 r_angle_refined_deg 1.394 r_mcbond_it 0.897 r_angle_other_deg 0.881 r_mcbond_other 0.237 r_chiral_restr 0.089 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1113 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing