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Methyltransferase domain of human PR domain-containing protein 10
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DB5 PDB entry 3DB5, 3EP0 experimental model PDB 3EP0 PDB entry 3DB5, 3EP0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 25% PEG3350, 0.2NH4oAC, Bis -6.5, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.41 49.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.864 α = 90 b = 94.864 β = 90 c = 76.769 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 2009-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID
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 2.5 30 25428
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 PDB entry 3DB5, 3EP0 2.5 94.86 22254 976 98.33 0.24407 0.24179 0.2498 0.2978 0.3104 RANDOM 24.711
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] -2.54 -2.54 5.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.53 r_dihedral_angle_4_deg 16.892 r_dihedral_angle_3_deg 16.331 r_dihedral_angle_1_deg 7.734 r_scangle_it 3.137 r_scbond_it 1.999 r_angle_refined_deg 1.742 r_mcangle_it 1.121 r_mcbond_it 0.612 r_chiral_restr 0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.53 r_dihedral_angle_4_deg 16.892 r_dihedral_angle_3_deg 16.331 r_dihedral_angle_1_deg 7.734 r_scangle_it 3.137 r_scbond_it 1.999 r_angle_refined_deg 1.742 r_mcangle_it 1.121 r_mcbond_it 0.612 r_chiral_restr 0.103 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3782 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling