Experiment: 4NHO

Structure of the spliceosomal DEAD-box protein Prp28

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DB3	PDB entry 2DB3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	298	2.2 M ammonium sulfate, 20 % (v/v) glycerol, 0.1 M CAPS, mixing 1 ul of protein with 1 ul of reservoir solution, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.85	56.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 125.43	α = 90
b = 136.77	β = 90
c = 73.22	γ = 90

Symmetry
Space Group	C 2 2 21

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 225 mm CCD	mirrors	2005-06-06	M	SINGLE WAVELENGTH
2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	1.001212	BESSY	14.1
2	SYNCHROTRON	BESSY BEAMLINE 14.1	1.008580	BESSY	14.1

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	39.97	100	0.064	12.1	4.9	42906	42906			32.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.11	100		0.584	0.652	2.3	4.9	6219

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	PDB entry 2DB3	2	28.825	1.34	42906	42839	2159	99.87	0.1943	0.1931	0.1955	0.2176	0.2212	RANDOM	59.0384

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]
24.5474			-11.2129		-13.3345

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	18.918
f_angle_d	1.276
f_chiral_restr	0.086
f_bond_d	0.012
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3505
Nucleic Acid Atoms
Solvent Atoms	220
Heterogen Atoms	52

Software

Software
Software Name	Purpose
SCALA	data scaling
SOLOMON	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
MOSFLM	data reduction
SHARP	phasing