9PCA | pdb_00009pca

HUMAN PRMT5:MEP50 COMPLEX IN COMPLEX WITH LIGAND 18


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7BO7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2770.27 M (NH4)2SO4; 0.05 M MES pH 6.75; 23.0% w/v PEG 3350 PROTEIN SOLUTION : 2 mM DTT, 10 % Glycerol, 10 mM HEPES-NaOH pH 7.5, 150 mM NaCl
Crystal Properties
Matthews coefficientSolvent content
3.0659.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.807α = 90
b = 139.139β = 90
c = 179.354γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2024-09-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.8856ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.197109.9452.60.2160.0620.9837.712.934528
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.1972.5417.51.8650.5470.5871.612.4

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 REPLACEMENTTHROUGHOUT2.2109.9432837169152.550.226120.224030.22470.266210.2664RANDOM42.156
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]
0.81-0.38-0.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.464
r_dihedral_angle_4_deg14.228
r_dihedral_angle_3_deg13.07
r_dihedral_angle_1_deg6.936
r_long_range_B_refined3.84
r_long_range_B_other3.832
r_mcangle_it2.373
r_mcangle_other2.373
r_scangle_other1.613
r_mcbond_other1.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.464
r_dihedral_angle_4_deg14.228
r_dihedral_angle_3_deg13.07
r_dihedral_angle_1_deg6.936
r_long_range_B_refined3.84
r_long_range_B_other3.832
r_mcangle_it2.373
r_mcangle_other2.373
r_scangle_other1.613
r_mcbond_other1.315
r_angle_refined_deg1.302
r_angle_other_deg1.053
r_scbond_it0.857
r_scbond_other0.857
r_chiral_restr0.044
r_bond_refined_d0.003
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7335
Nucleic Acid Atoms
Solvent Atoms149
Heterogen Atoms66

Software

Software
Software NamePurpose
autoPROCdata reduction
XDSdata reduction
autoPROCdata scaling
Aimlessdata scaling
REFMACrefinement
XDSdata scaling