2RFF | pdb_00002rff

Crystal structure of a putative nucleotidyltransferase (NP_343093.1) from Sulfolobus solfataricus at 1.40 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	277	NANODROP, 20.0% PEG MME2000, 0.1M Tris-HCl pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.85	33.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 25.007	α = 77.24
b = 29.884	β = 73.72
c = 35.202	γ = 78.3

Symmetry
Space Group	P 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	MARMOSAIC 300 mm CCD	Adjustable focusing mirrors in K-B geometry	2007-08-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.95373	APS	23-ID-D

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	1.4	33.278	90.5	0.064	13	3.7		16758

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.4	1.45	54		0.261		3	1000

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.4	33.278	16755	851	90.5	0.147	0.145	0.15	0.187	0.19	RANDOM	13.191

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]
-1.83	0.68	-0.2	-0.48	-2.13	3.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	22.395
r_dihedral_angle_4_deg	12.724
r_dihedral_angle_3_deg	10.88
r_sphericity_free	6.787
r_dihedral_angle_1_deg	4.859
r_scangle_it	4.508
r_sphericity_bonded	4.292
r_scbond_it	3.566
r_mcangle_it	3.056
r_mcbond_it	2.459
r_angle_refined_deg	1.807
r_rigid_bond_restr	1.592
r_angle_other_deg	1.429
r_mcbond_other	1.218
r_nbd_refined	0.228
r_symmetry_vdw_refined	0.177
r_nbtor_refined	0.166
r_nbd_other	0.16
r_symmetry_vdw_other	0.151
r_symmetry_hbond_refined	0.146
r_xyhbond_nbd_refined	0.111
r_chiral_restr	0.108
r_nbtor_other	0.073
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.005
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	990
Nucleic Acid Atoms
Solvent Atoms	107
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data reduction
SOLVE	phasing
SHELXD	phasing