2Q8V | pdb_00002q8v

NblA protein from T. vulcanus crystallized with urea

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OJH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	25% elthelene glycol, 2M Urea, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.265	α = 90
b = 43.265	β = 90
c = 149.4	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	CCD	ADSC QUANTUM 4			M	SINGLE WAVELENGTH
2	1	x-ray		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.97913	ESRF	BM30A
2	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.9792	ESRF	ID14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.5	50	99.8	0.073	19.1	6.2		6108		2.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.5	2.64	100		0.326	0.358	4.4	5.9	849

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD/Molecular Replacement	THROUGHOUT	1OJH	2.5	30	6108	984	100	0.245	0.2791	0.264	0.2767	random	36.4

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]
-6.085	-7.701		-6.085		12.17

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	20.2
c_improper_angle_d	1.72
c_angle_deg	1.09
c_bond_d	0.0096

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	843
Nucleic Acid Atoms
Solvent Atoms	16
Heterogen Atoms	8

Software

Software
Software Name	Purpose
DNA	data collection
CCP4	model building
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
CCP4	phasing