9MGR | pdb_00009mgr

Crystal structure of PRMT5:MEP50 in complex with MTA and compound 51


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8VEO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629110% PEG 4000, 0.1 M sodium citrate (pH 6.0), 0.2 M magnesium chloride
Crystal Properties
Matthews coefficientSolvent content
2.8456.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.946α = 90
b = 137.889β = 90
c = 178.607γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 S 9M2024-06-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL02U10.97918SSRFBL02U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.07109.1593.50.160.0450.99812.913.536863
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.072.36581.51.3430.420.7581.911.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.07109.1535038182547.640.22410.221650.22660.272730.2706RANDOM42.548
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]
0.46-0.38-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.888
r_dihedral_angle_1_deg7.25
r_dihedral_angle_2_deg5.608
r_long_range_B_refined4.455
r_long_range_B_other4.454
r_mcangle_it2.467
r_mcangle_other2.467
r_scangle_other1.845
r_mcbond_it1.37
r_mcbond_other1.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.888
r_dihedral_angle_1_deg7.25
r_dihedral_angle_2_deg5.608
r_long_range_B_refined4.455
r_long_range_B_other4.454
r_mcangle_it2.467
r_mcangle_other2.467
r_scangle_other1.845
r_mcbond_it1.37
r_mcbond_other1.37
r_angle_refined_deg1.005
r_scbond_it0.995
r_scbond_other0.995
r_angle_other_deg0.356
r_chiral_restr0.045
r_gen_planes_refined0.003
r_bond_refined_d0.002
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7313
Nucleic Acid Atoms
Solvent Atoms132
Heterogen Atoms125

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling
REFMACphasing