Experiment: 5E2B

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		isomorphous structure of NTMT1 in complex with different peptide

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	26% PEG3350, 16% tacsimate

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.268	α = 90
b = 107.268	β = 90
c = 205.604	γ = 120

Symmetry
Space Group	P 65 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	RIGAKU SATURN A200		2015-08-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.8	29.65	99.2	0.13	0.133	0.028	0.999	27.7	21.1		64736

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.84	98		1.18	1.208	0.257	0.87	3.6	21.1	3713

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	FOURIER SYNTHESIS	THROUGHOUT	isomorphous structure of NTMT1 in complex with different peptide	1.95	29.65	49282	2019	99.31	0.1537	0.1524	0.1673	0.1875	0.1964	THIN SHELLS (SFTOOLS)	18.6

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]
0.14	0.07		0.14		-0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.292
r_dihedral_angle_4_deg	18.934
r_dihedral_angle_3_deg	12.196
r_dihedral_angle_1_deg	6.172
r_angle_refined_deg	1.766
r_angle_other_deg	1.339
r_mcangle_it	0.913
r_mcbond_it	0.539
r_mcbond_other	0.533
r_chiral_restr	0.114

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.292
r_dihedral_angle_4_deg	18.934
r_dihedral_angle_3_deg	12.196
r_dihedral_angle_1_deg	6.172
r_angle_refined_deg	1.766
r_angle_other_deg	1.339
r_mcangle_it	0.913
r_mcbond_it	0.539
r_mcbond_other	0.533
r_chiral_restr	0.114
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3642
Nucleic Acid Atoms
Solvent Atoms	385
Heterogen Atoms	115

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.