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Crystal structure of human P100 tudor domain conserved region
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HQE PDB ENTRY 2HQE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MODIFIED MICROBATCH 7.9 291 1.0 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (11.0 MG/ML) AND RESERVOIR SOLUTION CONTAINING 1.06M AMMONIUM SULFATE, 200.0 MM LITHIUM SULFATE, 0.1M TRIS PH 7.9, MODIFIED MICROBATCH, temperature 291K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.777 α = 90.03 b = 37.684 β = 105.32 c = 40.202 γ = 99.72
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 MARMOSAIC 300 mm CCD ROSENBAUM 2005-12-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.9790 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 1.42 38.72 82.17 0.05 15.6 3.4 27043 25303 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.42 1.46 23.08 0.03 1.3 212
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION PT-SAS THROUGHOUT PDB ENTRY 2HQE 1.42 38.72 25303 25303 1348 82.17 0.23163 0.22947 0.27042 RANDOM 16.11
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] 0.33 -0.09 0.02 -0.18 -0.11 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.932 r_dihedral_angle_4_deg 23.885 r_dihedral_angle_3_deg 13.104 r_dihedral_angle_1_deg 4.761 r_scangle_it 3.449 r_scbond_it 2.306 r_mcangle_it 1.348 r_angle_refined_deg 1.21 r_mcbond_it 0.81 r_xyhbond_nbd_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.932 r_dihedral_angle_4_deg 23.885 r_dihedral_angle_3_deg 13.104 r_dihedral_angle_1_deg 4.761 r_scangle_it 3.449 r_scbond_it 2.306 r_mcangle_it 1.348 r_angle_refined_deg 1.21 r_mcbond_it 0.81 r_xyhbond_nbd_refined 0.323 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.276 r_nbd_refined 0.245 r_symmetry_hbond_refined 0.197 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1378 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling SCA2STRUCTURE phasing