1SYX | pdb_00001syx

The crystal structure of a binary U5 snRNP complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QGV	PDB ENTRY 1QGV and 1GYF
experimental model	PDB	1GYF	PDB ENTRY 1QGV and 1GYF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	PEG 2000mme, MES, calcium acetate, 1,4-butanediol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.726	α = 90
b = 75.913	β = 94.27
c = 77.027	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MARRESEARCH	mirrors	2003-03-01	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MARRESEARCH	mirrors	2003-08-24	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418
2	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.8000	EMBL/DESY, HAMBURG	X13

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.345	50	100	0.031		2.4	30397	30397

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	2.345	2.39	92.5		0.248	2.4	2.4	1535

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1QGV and 1GYF	2.345	49.39	30297	28709	1486	91.84	0.217	0.21806	0.21578	0.2139	0.26249	0.2578	RANDOM	40.592

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_1_deg	5.715
r_scangle_it	1.878
r_scbond_it	1.177
r_angle_refined_deg	1.07
r_mcangle_it	0.774
r_mcbond_it	0.405
r_symmetry_hbond_refined	0.222
r_nbd_refined	0.199
r_xyhbond_nbd_refined	0.177
r_symmetry_vdw_refined	0.173
r_chiral_restr	0.074
r_gen_planes_other	0.04
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4890
Nucleic Acid Atoms
Solvent Atoms	192
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
MOLREP	phasing
CNS	refinement
DENZO	data reduction