3K7U | pdb_00003k7u

Structure of essential protein from Trypanosoma brucei

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3K80	PDB entry 3K80

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	25% PEG2000, 0.1 M Bis-tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.362	α = 90
b = 50.359	β = 108.97
c = 44.15	γ = 90

Symmetry
Space Group	C 1 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	77	CCD	MARMOSAIC 325 mm CCD		2009-06-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.9795	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.1	50	96.4	0.045	30.6	3.8		15229			40.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.99	2.06	76.2		0.504	3.1	3.8	15229

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3K80	2.1	29.69	14154	14154	752	98.62	0.20538	0.20219	0.2267	0.26459	0.2857	RANDOM	25.722

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]
0.06		-0.07	0.18		-0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.048
r_dihedral_angle_4_deg	18.746
r_dihedral_angle_3_deg	16.406
r_dihedral_angle_1_deg	6.892
r_scangle_it	4.152
r_scbond_it	2.729
r_mcangle_it	1.965
r_angle_refined_deg	1.842
r_mcbond_it	1.107
r_angle_other_deg	1
r_mcbond_other	0.279
r_chiral_restr	0.12
r_bond_refined_d	0.022
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1668
Nucleic Acid Atoms
Solvent Atoms	70
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling