6NT2 | pdb_00006nt2

type 1 PRMT in complex with the inhibitor GSK3368715

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	SAH and inhibitor were added to PRMT1 to a final concentration of 1.5mM each (3% DMSO). The complex was incubated at 4deg C before crystallization. 1uL protein-ligand complex was mixed with 1 uL of reservoir solution containing 0.3M sodium formate, 0.1M HEPES, 8% PEG 10,000, pH 6.5, and 0.2 uL 30% sodium dextran sulfate Mr=5,000). The droplets were incubated against 500uL reservoir solution for 1-2 days before crystals were observed.

Crystal Properties
Matthews coefficient	Solvent content
3.17	61.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 174.15	α = 90
b = 174.15	β = 90
c = 142.35	γ = 90

Symmetry
Space Group	P 41 21 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		2013-08-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.0000	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	2.48	38.94	100	0.179	0.189	0.06	0.996	12.7	9.9		77777

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	2.48	2.51	100		0.961	1.013	0.319	0.81	2.7	10.1

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	2.48	38.94	73795	3909	99.95	0.19183	0.19026	0.2022	0.22169	0.2315	RANDOM	22.078

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]
0.54			0.54		-1.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.506
r_dihedral_angle_4_deg	14.655
r_dihedral_angle_3_deg	13.001
r_dihedral_angle_1_deg	5.938
r_long_range_B_refined	3.087
r_long_range_B_other	3.015
r_angle_refined_deg	1.196
r_angle_other_deg	0.851
r_mcangle_it	0.768
r_mcangle_other	0.768
r_scangle_other	0.595
r_mcbond_it	0.41
r_mcbond_other	0.41
r_scbond_it	0.326
r_scbond_other	0.324
r_chiral_restr	0.067
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10732
Nucleic Acid Atoms
Solvent Atoms	664
Heterogen Atoms	354

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing