2GHP | pdb_00002ghp

Crystal structure of the N-terminal 3 RNA binding domains of the yeast splicing factor Prp24

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.0003 M TCEP, 0.005 TRIS PH 8.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (14% MEPEG 5000, 0.20 M TETRAMETHYL AMMONIUM CHLORIDE, 0.10 M SODIUM SUCCINATE PH 4.0) Crystals cryo-protected with the well solution supplemented with 30% ethylene glycol., VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.608	α = 90
b = 125.848	β = 90
c = 196.542	γ = 90

Symmetry
Space Group	P 21 21 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 300 mm CCD	HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR	2005-10-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.97911	APS	22-ID

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	2.7	49.503	94.2	0.122	7.416	7		74236

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	2.7	2.8	74.3		0.489	2.39	5.4	5801

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.7	49.503	74155	3738	94.218	0.216	0.213	0.2206	0.2642	0.268	random	56.783

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]
-2.223			5.883		-3.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.723
r_dihedral_angle_3_deg	20.165
r_dihedral_angle_4_deg	19.817
r_dihedral_angle_1_deg	5.966
r_scangle_it	4.851
r_scbond_it	3.112
r_mcangle_it	1.681
r_angle_refined_deg	1.38
r_mcbond_it	0.884
r_nbtor_refined	0.312
r_symmetry_vdw_refined	0.238
r_nbd_refined	0.213
r_symmetry_hbond_refined	0.157
r_xyhbond_nbd_refined	0.138
r_chiral_restr	0.096
r_bond_refined_d	0.012
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15026
Nucleic Acid Atoms
Solvent Atoms	193
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing
SHELXD	phasing
ARP/wARP	model building