9MGN | pdb_00009mgn

Crystal structure of PRMT5:MEP50 in complex with MTA and compound 41

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		A previously determined proprietary structure (which was ultimately derived from PDB entry 8VEO) provided the initial phases.

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
2.81	56.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.65	α = 90
b = 137.84	β = 90
c = 179.09	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 EIGER X 9M		2019-03-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.07812	APS	21-ID-D

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	2.82	44.8	98.9	0.122	0.126	0.034	0.998	14.2	13.5		30319

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	2.82	2.89		98.4	1.154	1.197	0.317	0.924		14.1

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	FOURIER SYNTHESIS	THROUGHOUT	2.82	44.8	28805	1500	98.73	0.23134	0.22868	0.2433	0.28094	0.2925	RANDOM	86.3

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]
14.11			-1.25		-12.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.075
r_dihedral_angle_3_deg	16.563
r_dihedral_angle_4_deg	16.198
r_dihedral_angle_1_deg	7.611
r_mcangle_it	3.375
r_mcangle_other	3.374
r_scangle_other	2.549
r_mcbond_it	1.902
r_mcbond_other	1.902
r_scbond_it	1.385
r_scbond_other	1.385
r_angle_refined_deg	1.292
r_angle_other_deg	1.081
r_chiral_restr	0.044
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	7391
Nucleic Acid Atoms
Solvent Atoms	6
Heterogen Atoms	69

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
REFMAC	phasing