3BNW

Crystal structure of riboflavin kinase from Trypanosoma brucei

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model		Hybrid model generated by Rosetta

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.6	290	20% PEG 3350, 0.28M KF, 0.1M HEPES, 5mM DTT, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
1.92	36.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.695	α = 90
b = 65.604	β = 103.49
c = 62.69	γ = 90

Symmetry
Space Group	P 1 21 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 325 mm CCD		2005-06-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97915	SSRL	BL9-2

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	2.4	38.6	88	0.064	10.9	3.3	10719	10719			52

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-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Hybrid model generated by Rosetta	2.4	20	10179	510	86.73	0.21616	0.2128	0.28857	RANDOM	25.677

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]
-0.47		0.01	1.11		-0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.07
r_dihedral_angle_3_deg	13.978
r_dihedral_angle_4_deg	13.42
r_dihedral_angle_1_deg	5.622
r_scangle_it	1.017
r_angle_refined_deg	0.961
r_angle_other_deg	0.765
r_mcangle_it	0.719
r_scbond_it	0.713
r_mcbond_it	0.422
r_nbtor_refined	0.181
r_nbd_refined	0.172
r_nbd_other	0.172
r_symmetry_vdw_other	0.166
r_symmetry_hbond_refined	0.162
r_xyhbond_nbd_refined	0.136
r_symmetry_vdw_refined	0.107
r_nbtor_other	0.082
r_mcbond_other	0.056
r_chiral_restr	0.055
r_bond_refined_d	0.006
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2494
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing