9ATV | pdb_00009atv

X-ray co-crystal structure of NCGC00685960 / NCATS-SM9335 in NNMT

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	0.15 M DL-Malic acid pH 7.0, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.596	α = 90
b = 91.596	β = 90
c = 213.257	γ = 120

Symmetry
Space Group	P 32 2 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	PIXEL	DECTRIS PILATUS 6M		2019-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.9793	ALBA	XALOC

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	2.41	50	99	0.999	16.3	5.4		40333

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	2.41	2.5	99.1		0.939

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	2.413	45.798	40287	1922	98.912	0.198	0.1965	0.2007	0.2343	0.2396	70.917

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]
-0.107	-0.054		-0.107		0.348

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.789
r_dihedral_angle_6_deg	10.664
r_dihedral_angle_1_deg	6.388
r_dihedral_angle_2_deg	4.205
r_lrange_it	3.571
r_lrange_other	3.561
r_scangle_it	2.174
r_scangle_other	2.174
r_mcangle_it	1.967
r_mcangle_other	1.966
r_scbond_it	1.255
r_scbond_other	1.255
r_mcbond_it	1.139
r_mcbond_other	1.138
r_angle_refined_deg	1.08
r_angle_other_deg	0.345
r_nbd_refined	0.192
r_symmetry_nbd_other	0.186
r_nbtor_refined	0.176
r_symmetry_nbd_refined	0.153
r_nbd_other	0.146
r_xyhbond_nbd_refined	0.109
r_symmetry_xyhbond_nbd_refined	0.081
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.045
r_symmetry_xyhbond_nbd_other	0.042
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6197
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms	93

Software

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