Experiment: 9MG0

Structure of Kluyveromyces lactis mRNA cap (guanine-N7) methyltransferase, Abd1, in complex with SAH

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2HV9	Encephalitozoon cuniculi mRNA Cap (Guanine-N7) Methyltransferase in complex with sinefungin

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		292	0.2 M Calcium Chloride, 20% (w/v) PEG 3350, and 0.1 M Potassium Sodium Tartrate

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.616	α = 90
b = 64.821	β = 94.48
c = 73.524	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	ADSC QUANTUM 315		2015-10-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.075	NSLS	X29A

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	1.3	50	98.6	0.059	12.4	4		143920

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	1.3	1.32	97.2		0.702		3.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.3	24.96	1.34	143728	7303	98.25	0.1665	0.1654	0.166	0.1867	0.1858

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.236
f_angle_d	0.992
f_chiral_restr	0.081
f_plane_restr	0.014
f_bond_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4676
Nucleic Acid Atoms
Solvent Atoms	575
Heterogen Atoms	116

Software

Software
Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
HKL-2000	data reduction
PHASER	phasing