3FSD | pdb_00003fsd

Crystal structure of NTF2-like protein of unknown function in nutrient uptake (YP_427473.1) from RHODOSPIRILLUM RUBRUM ATCC 11170 at 1.70 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	20.0% polyethylene glycol 3350, 0.2M magnesium chloride, ADDITIVE: 0.001M uridine 5'-monophosphate (UMP), NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K.

Crystal Properties
Matthews coefficient	Solvent content
1.8	31.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.018	α = 90
b = 61.018	β = 90
c = 56.442	γ = 90

Symmetry
Space Group	P 42 21 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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2008-11-13	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.97867,0.97776,0.91162	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.7	27.287	100	0.095	0.095	15.8	9.4		12272			20.479

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)
1	1.7	1.74	100		0.755	0.755	2.4	9.6	884

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	MAD	THROUGHOUT	1.7	27.287	12236	585	99.95	0.175	0.172	0.17	0.221	0.22	RANDOM	24.583

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]
-1.23			-1.23		2.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.878
r_dihedral_angle_4_deg	14.51
r_dihedral_angle_3_deg	12.759
r_scangle_it	7.041
r_dihedral_angle_1_deg	5.694
r_scbond_it	5.513
r_mcangle_it	3.556
r_mcbond_it	2.556
r_angle_refined_deg	1.684
r_angle_other_deg	0.984
r_mcbond_other	0.633
r_symmetry_vdw_other	0.309
r_xyhbond_nbd_refined	0.218
r_nbd_other	0.214
r_nbd_refined	0.189
r_symmetry_hbond_refined	0.18
r_nbtor_refined	0.173
r_symmetry_vdw_refined	0.166
r_chiral_restr	0.094
r_nbtor_other	0.09
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	927
Nucleic Acid Atoms
Solvent Atoms	93
Heterogen Atoms	18

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing