8G2F | pdb_00008g2f

Crystal Structure of PRMT3 with Compound II710

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2FYT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	20% PEG3350, 0.3 M Sodium Formate

Crystal Properties
Matthews coefficient	Solvent content
2.86	57.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.733	α = 90
b = 70.733	β = 90
c = 175.262	γ = 90

Symmetry
Space Group	P 43 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	PIXEL	DECTRIS EIGER2 X 16M		2021-03-16	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	2.06	50	97.4	0.09	1	8.9	10.4		27517

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	2.06	2.1	81.6		0.841	0.915	1.7	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	2.06	48.14	26354	1088	97.06	0.20883	0.20695	0.21	0.25598	0.26	RANDOM	54.369

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]
3.09			3.09		-6.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.746
r_dihedral_angle_4_deg	23.539
r_dihedral_angle_3_deg	16.664
r_long_range_B_other	7.718
r_long_range_B_refined	7.712
r_dihedral_angle_1_deg	7.525
r_scangle_other	6.464
r_mcangle_it	5.419
r_mcangle_other	5.419
r_scbond_it	4.796
r_scbond_other	4.794
r_mcbond_it	4.233
r_mcbond_other	4.233
r_angle_refined_deg	1.358
r_angle_other_deg	1.243
r_chiral_restr	0.057
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
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	2338
Nucleic Acid Atoms
Solvent Atoms	42
Heterogen Atoms	33

Software

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