8G2H | pdb_00008g2h

Crystal Structure of PRMT4 with Compound YD1113

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5U4X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	0.2 M Calcium chloride dihydrate, 0.05 M HEPES sodium pH 7.5, 28% v/v Polyethylene glycol 400, 0.002 M Spermine

Crystal Properties
Matthews coefficient	Solvent content
3.26	62.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.215	α = 90
b = 84.215	β = 90
c = 130.426	γ = 120

Symmetry
Space Group	P 32 2 1

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 X 16M		2022-06-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.97918	APS	24-ID-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.49	50	100	0.065	0.998	12.6	8.2		87534

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.49	1.52	100		0.945	0.75	2	8.1

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	1.49	48.66	85796	1683	99.7	0.17147	0.17134	0.18	0.17745	0.19	RANDOM	19.547

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]
0.21	0.11		0.21		-0.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.597
r_dihedral_angle_4_deg	18.723
r_dihedral_angle_3_deg	12.683
r_dihedral_angle_1_deg	6.331
r_long_range_B_refined	5.255
r_long_range_B_other	4.914
r_scangle_other	3.71
r_scbond_it	2.41
r_scbond_other	2.409
r_mcangle_it	2.064
r_mcangle_other	2.063
r_angle_refined_deg	1.47
r_angle_other_deg	1.448
r_mcbond_it	1.391
r_mcbond_other	1.391
r_chiral_restr	0.079
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	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	2652
Nucleic Acid Atoms
Solvent Atoms	185
Heterogen Atoms	50

Software

Software
Software Name	Purpose
HKL-3000	data scaling
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction