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)
Type	Source	Accession Code	Details
experimental model	PDB	8VEO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	291	10% PEG 4000, 0.1 M sodium citrate (pH 6.0), 0.2 M magnesium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.946	α = 90
b = 137.889	β = 90
c = 178.607	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	PIXEL	DECTRIS EIGER2 S 9M		2024-06-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL02U1	0.97918	SSRF	BL02U1

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.07	109.15	93.5	0.16	0.045	0.998	12.9	13.5		36863

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)	Redundancy	Number Unique Reflections (All)
1	2.07	2.365	81.5		1.343	0.42	0.758	1.9	11.1

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.07	109.15	35038	1825	47.64	0.2241	0.22165	0.2266	0.27273	0.2706	RANDOM	42.548

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
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.888
r_dihedral_angle_1_deg	7.25
r_dihedral_angle_2_deg	5.608
r_long_range_B_refined	4.455
r_long_range_B_other	4.454
r_mcangle_it	2.467
r_mcangle_other	2.467
r_scangle_other	1.845
r_mcbond_it	1.37
r_mcbond_other	1.37
r_angle_refined_deg	1.005
r_scbond_it	0.995
r_scbond_other	0.995
r_angle_other_deg	0.356
r_chiral_restr	0.045
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7313
Nucleic Acid Atoms
Solvent Atoms	132
Heterogen Atoms	125

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
REFMAC	phasing