3H4C | pdb_00003h4c

Structure of the C-terminal Domain of Transcription Factor IIB from Trypanosoma brucei

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	298	24% PEG 3350, 0.2M sodium chloride, 0.1M Bis-tris (2-Bis(2-hydroxyethyl)amino-2-(hydroxymethyl)-1,3-propanediol), pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.233	α = 90
b = 109.233	β = 90
c = 51.123	γ = 90

Symmetry
Space Group	P 43 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	110	IMAGE PLATE	RIGAKU RAXIS IV++	VariMax	2008-06-10	M	SINGLE WAVELENGTH
2	1	x-ray	110	CCD	ADSC QUANTUM 315r	mirrors	2008-08-11	M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418
2	SYNCHROTRON	NSLS BEAMLINE X29A	0.9791,0.9793,0.9700	NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.3	50	94.8			13573	13573

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	2.3	2.38	94.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	2.3	7.99	13203	11861	1342	95.2	0.20831	0.20831	0.2037	0.21	0.24938	0.25	RANDOM	19.7

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.402
r_dihedral_angle_4_deg	16.282
r_dihedral_angle_3_deg	13.031
r_dihedral_angle_1_deg	3.806
r_scangle_it	1.895
r_scbond_it	1.115
r_angle_refined_deg	1.065
r_mcangle_it	0.59
r_mcbond_it	0.299
r_chiral_restr	0.063

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.402
r_dihedral_angle_4_deg	16.282
r_dihedral_angle_3_deg	13.031
r_dihedral_angle_1_deg	3.806
r_scangle_it	1.895
r_scbond_it	1.115
r_angle_refined_deg	1.065
r_mcangle_it	0.59
r_mcbond_it	0.299
r_chiral_restr	0.063
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1609
Nucleic Acid Atoms
Solvent Atoms	56
Heterogen Atoms	4

Software

Software
Software Name	Purpose
ADSC	data collection
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.