5C9Z | pdb_00005c9z

Crystal structure of PRMT5:MEP50 with EPZ015866 and sinefungin

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.1	293	0.2 M Sodium acetate, 0.1 M Sodium citrate pH 6.1, 10% w/v PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
3	59.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.81	α = 90
b = 137.78	β = 90
c = 178.91	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	CCD	MARMOSAIC 300 mm CCD		2013-03-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.36	89.46	99.4	0.048	18.4	5		52114

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.36	2.42	99.7		0.607	2.3	5.1

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		THROUGHOUT	2.36	82.53	49452	2659	99.22	0.2392	0.2366	0.2364	0.2881	0.289	RANDOM	60.484

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]
6.46			-1.22		-5.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.968
r_dihedral_angle_4_deg	16.376
r_dihedral_angle_3_deg	15.694
r_dihedral_angle_1_deg	5.41
r_mcangle_it	3.036
r_mcbond_it	1.722
r_scbond_it	1.425
r_angle_refined_deg	0.98
r_chiral_restr	0.065
r_bond_refined_d	0.005
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7427
Nucleic Acid Atoms
Solvent Atoms	123
Heterogen Atoms	61

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction