9UL8 | pdb_00009ul8

Cryogenic temperature crystal structure of Nmar_1308 protein at 2.46 angstrom resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7EUM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		298	0.3M Magnesium chloride hexahydrate, 0.3M Calcium chloride dihydrate, 1.0M Tris (base), BICINE pH 8.5, 40% v/v PEG 500* MME, 20% w/v PEG 2000

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.97	α = 90
b = 75.97	β = 90
c = 209.42	γ = 120

Symmetry
Space Group	P 31 1 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	PIXEL	DECTRIS EIGER X 9M		2023-11-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL32XU	1	SPring-8	BL32XU

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	2.46	37.99	100	0.99	10.17	2		25601

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	2.46	2.61			0.5

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	2.46	37.99	1.37	25543	2007	99.99	0.3806	0.3784	0.3789	0.4068	0.4069

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	6.281
f_angle_d	0.904
f_chiral_restr	0.049
f_plane_restr	0.008
f_bond_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5473
Nucleic Acid Atoms
Solvent Atoms	35
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing