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Crystal structure of Human Protein Arginine Methyltransferase 9 (PRMT9)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4C4A PHENIX.MR_ROSETTA with PDB entry 4C4A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 20% PEG3350, 0.2M ammonium nitrate
Crystal Properties Matthews coefficient Solvent content 2.19 43.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.812 α = 90 b = 83.802 β = 98.16 c = 65.711 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 PIXEL DECTRIS EIGER X 16M 2019-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.4 65.05 98.7 0.072 0.085 0.045 0.998 11 3.4 27005 69.14
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 94.7 1.208 1.419 0.739 0.468 3.6
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PHENIX.MR_ROSETTA with PDB entry 4C4A 2.45 65 25460 1310 99 0.219 0.216 0.2304 0.26 0.273 66.62
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] -3.478 13.2393 -2.1813 5.6593
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 12.63 t_omega_torsion 3.6 t_angle_deg 1.19 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 12.63 t_omega_torsion 3.6 t_angle_deg 1.19 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4469 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 13
Software Software Software Name Purpose Aimless data scaling BUSTER refinement PDB_EXTRACT data extraction XDS data reduction MR-Rosetta phasing