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Methyltransferase domain of human PR domain-containing protein 1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 Purified PRDM1 was crystallized using hanging drop vapor diffusion method at
20 C by mixing 1.5 l of the protein solution with 1.5 l of the reservoir
solution containing 2.0 M Na Formide, 0.1 M sodium acetate, pH 4.6., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.63 53.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.834 α = 90 b = 64.96 β = 90 c = 112.663 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1.28268 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.65 50 99.8 0.061 10.5 6.1 57924
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) 1.65 1.68 98.5 0.664 4.3 2783
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 1.65 50 57644 2930 99.4 0.197 0.196 0.1922 0.217 0.2142 RANDOM 22.253
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] 0.34 -0.05 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.035 r_dihedral_angle_4_deg 15.941 r_dihedral_angle_3_deg 12.643 r_dihedral_angle_1_deg 6.435 r_scangle_it 4.609 r_scbond_it 3.019 r_mcangle_it 1.918 r_angle_refined_deg 1.571 r_mcbond_it 1.294 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.035 r_dihedral_angle_4_deg 15.941 r_dihedral_angle_3_deg 12.643 r_dihedral_angle_1_deg 6.435 r_scangle_it 4.609 r_scbond_it 3.019 r_mcangle_it 1.918 r_angle_refined_deg 1.571 r_mcbond_it 1.294 r_nbtor_refined 0.311 r_symmetry_vdw_refined 0.221 r_nbd_refined 0.211 r_xyhbond_nbd_refined 0.148 r_symmetry_hbond_refined 0.13 r_chiral_restr 0.124 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2892 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction PHASES phasing