4PKD | pdb_00004pkd

U1-70k in complex with U1 snRNA stem-loops 1 and U1-A RRM in complex with stem-loop 2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1URN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	293	40% MPD, 0.15 M sodium chloride, 0.1 M sodium acetate, pH 4.2

Crystal Properties
Matthews coefficient	Solvent content
2.34	53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.22	α = 90
b = 66.6	β = 110.95
c = 93.73	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	PIXEL	PSI PILATUS 6M		2011-10-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	1.0332	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.5	87.54	99.1	0.076	0.047	11	3.7	16115	15967

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	2.5	2.64	99.4		0.35	3.2	3.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	MOLECULAR REPLACEMENT	THROUGHOUT	1URN	2.5	87	15156	812	99.07	0.19992	0.19675	0.2	0.25791	0.26	RANDOM	50.252

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]
3.18		-0.12	0.23		-2.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.277
r_dihedral_angle_4_deg	19.822
r_dihedral_angle_3_deg	19.723
r_long_range_B_refined	8.964
r_long_range_B_other	8.963
r_dihedral_angle_1_deg	6.87
r_scangle_other	5.608
r_mcangle_it	4.168
r_mcangle_other	4.166
r_scbond_it	3.636
r_scbond_other	3.635
r_angle_other_deg	3.142
r_mcbond_it	2.735
r_mcbond_other	2.735
r_angle_refined_deg	1.91
r_chiral_restr	0.12
r_bond_refined_d	0.019
r_gen_planes_refined	0.014
r_bond_other_d	0.013
r_gen_planes_other	0.008
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1954
Nucleic Acid Atoms	1177
Solvent Atoms	113
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement