3U1U | pdb_00003u1u

Crystal structure of RNA polymerase-associated protein RTF1 homolog Plus-3 domain

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	sitting drop vapor diffusion	5.5	291	25% PEG-3350, 0.2M ammonium sulfate, 0.1M sodium cacodylate, pH 5.5, sitting drop vapor diffusion, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.7	53.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.479	α = 90
b = 50.369	β = 103.37
c = 69.776	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
xds	1	100
1	1	x-ray		IMAGE PLATE	RIGAKU RAXIS		2011-08-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E	1.5418

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	1.8	30	99.86	0.076	18.0335	7.2	29993	29882

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)
1	1.8	1.9	99.51		0.89		7.07	4298

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	SAD	THROUGHOUT	1.8	28.54	29923	29857	1513	99.78	0.2036	0.2018	0.2073	0.2349	0.2381	THIN SHELLS (SFTOOLS)	27.0878

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]
0.78		-0.6	0.27		-1.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.349
r_dihedral_angle_4_deg	18.832
r_dihedral_angle_3_deg	12.591
r_dihedral_angle_1_deg	6.132
r_scangle_it	3.398
r_scbond_it	2.146
r_angle_refined_deg	1.355
r_mcangle_it	1.193
r_angle_other_deg	0.881
r_mcbond_it	0.683
r_mcbond_other	0.192
r_chiral_restr	0.078
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2071
Nucleic Acid Atoms
Solvent Atoms	103
Heterogen Atoms	49

Software

Software
Software Name	Purpose
SCALA	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
JDirector	data collection
XDS	data reduction
ARP/wARP	model building
Coot	model building