Experiment: 7D8F

The crystal structure of ScNTM1 in complex with SAH

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2EX4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	291	2.8M sodium acetate trihydrate pH 7.0, 3.5M sodium formate pH 7.0, 20% PEG3350,0.2M magnesium nitrate hexahydrate

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.402	α = 90
b = 52.148	β = 90
c = 120.017	γ = 90

Symmetry
Space Group	P 21 21 21

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 16M		2019-03-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.97853	SSRF	BL17U

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	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	1.1	50	89.7	0.064	0.018	0.997	28.6	12.8		88586			10.4

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	1.1	1.12	42		0.559		3.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	2EX4	1.15	23.91	1.36	82645	4155	95.38	0.123	0.1221	0.123	0.1398	0.1404	14.96

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	19.8728
f_angle_d	1.0582
f_chiral_restr	0.0807
f_plane_restr	0.0072
f_bond_d	0.0069

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1851
Nucleic Acid Atoms
Solvent Atoms	269
Heterogen Atoms	26

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing