9R8Z | pdb_00009r8z

METTL3/14 complex with switchable fragment

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5IL1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	291	10% w/v PEG 4000, 20% v/v glycerol, 0.1 M bicine/Trizma base pH, 8.5 0.02 M 1,6-hexanediol, 0.02 M 1-butanol, 0.02 M (RS)-1,2- propanediol, 0.02 M 2-propanol, 0.02 M 1,4-butanediol, 0.02 M 1,3-propanediol

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.83	α = 90
b = 100.83	β = 90
c = 117.7	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	PIXEL	DECTRIS EIGER X 9M		2019-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91587	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.21	76.57	100	0.999	14.7	13		31097

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.21	2.27	100		0.606		13.6

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.21	76.57	31037	1544	99.958	0.177	0.1739	0.1835	0.2271	0.1912	61.864

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]
0.824			0.824		-1.647

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.115
r_dihedral_angle_6_deg	15.38
r_lrange_other	11.426
r_lrange_it	11.411
r_dihedral_angle_2_deg	10.371
r_scangle_it	9.241
r_scangle_other	9.239
r_dihedral_angle_1_deg	8.313
r_mcangle_it	6.979
r_mcangle_other	6.977
r_scbond_it	6.905
r_scbond_other	6.904
r_mcbond_it	5.186
r_mcbond_other	5.16
r_angle_refined_deg	2.594
r_angle_other_deg	0.879
r_nbd_refined	0.219
r_symmetry_nbd_other	0.21
r_nbtor_refined	0.189
r_xyhbond_nbd_refined	0.177
r_symmetry_nbd_refined	0.171
r_nbd_other	0.165
r_symmetry_xyhbond_nbd_refined	0.157
r_chiral_restr	0.126
r_symmetry_nbtor_other	0.094
r_symmetry_xyhbond_nbd_other	0.089
r_bond_refined_d	0.016
r_gen_planes_refined	0.013
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3957
Nucleic Acid Atoms
Solvent Atoms	228
Heterogen Atoms	35

Software

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