2NXP | pdb_00002nxp

Structure of NTD2 domain of the human TAF5 subunit of TFIID

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.1	295	0.1M Tris-HCl, 0.6M calcium chloride, 20% PEG 4000, pH 7.1, VAPOR DIFFUSION, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.62	α = 90
b = 61.829	β = 105.16
c = 133.357	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		CCD	ADSC QUANTUM 210	KOHZU: Double Crystal Si(111)	2005-10-25	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	0.9797, 1.0199	ALS	8.3.1

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	2.2	64.4	97.8	0.102	9.3	4.3	78392	76736	2	2	38.2

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)
	2.2		97.9		0.065	2.5	4.3

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 (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	2.17	64.42	76736	72912	3837	97.89	0.21507	0.21257	0.22	0.26252	0.27	RANDOM	35.522

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	34.441
r_dihedral_angle_3_deg	12.129
r_dihedral_angle_4_deg	10.597
r_dihedral_angle_1_deg	4.379
r_angle_refined_deg	0.722
r_angle_other_deg	0.6
r_symmetry_vdw_refined	0.234
r_symmetry_vdw_other	0.221
r_symmetry_hbond_refined	0.221
r_nbd_refined	0.212
r_xyhbond_nbd_refined	0.212
r_nbtor_refined	0.193
r_nbd_other	0.176
r_metal_ion_refined	0.127
r_symmetry_metal_ion_refined	0.118
r_nbtor_other	0.09
r_chiral_restr	0.047
r_bond_refined_d	0.004
r_gen_planes_refined	0.002
r_gen_planes_other	0.001
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9986
Nucleic Acid Atoms
Solvent Atoms	521
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
MOSFLM	data reduction
CCP4	data scaling
MLPHARE	phasing