5E1M | pdb_00005e1m

Crystal structure of NTMT1 in complex with PPKRIA peptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		isomorphous crystal structure of same protein.

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	59.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.406	α = 90
b = 107.406	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		2015-06-22	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	1.75	29.68	100	0.108	0.111	0.024	0.999	27	20.6		71201

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	1.75	1.78	99.9		0.942	0.966	0.21	0.91	4.3	20.4	3848

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 crystal structure of same protein.	1.75	29.68	68505	2625	99.9	0.1621	0.1611	0.1757	0.1882	0.1972	THIN SHELLS (SFTOOLS)	18.374

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]
					0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.978
r_dihedral_angle_4_deg	17.895
r_dihedral_angle_3_deg	11.332
r_dihedral_angle_1_deg	6.244
r_angle_refined_deg	1.758
r_angle_other_deg	1.061
r_mcangle_it	0.907
r_mcbond_it	0.548
r_mcbond_other	0.54
r_chiral_restr	0.115
r_bond_refined_d	0.017
r_gen_planes_refined	0.01
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3644
Nucleic Acid Atoms
Solvent Atoms	417
Heterogen Atoms	113

Software

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