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PRMT5 bound to PBM peptide from Riok1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GQB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 281 30% PEG 3350
200 mM ammonium sulfate
0.05% w/v dodecyl-maltoside
Crystal Properties Matthews coefficient Solvent content 3 58.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.96 α = 90 b = 139.41 β = 90 c = 179.95 γ = 90
Symmetry Space Group I 2 2 2
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 MARRESEARCH 2017-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.11 47.75 99.9 0.0119 0.998 10.65 6.3 76646 52.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.11 2.22 99.6 0.436 0.85 4.6
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4GQB 2.11 47.75 76646 3833 99.9 0.204 0.203 0.203 0.235 0.241 RANDOM 60.05
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] 3.8265 -16.8607 13.0342
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.7 t_omega_torsion 3.49 t_angle_deg 1.12 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 17.7 t_omega_torsion 3.49 t_angle_deg 1.12 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 7368 Nucleic Acid Atoms Solvent Atoms 509 Heterogen Atoms 27
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction