2QKL

The crystal structure of fission yeast mRNA decapping enzyme Dcp1-Dcp2 complex

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	0.1 M Ammonium Acetate and 5% PEG3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.723	α = 90
b = 49.665	β = 90
c = 115.052	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				2005-10-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	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	2.33	20	99.9	0.081	7.6	9.9	12284	11066	2	2

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	2.33	2.39	99.5		0.345	2.2	9.5

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.33	20	12284	10983	563	99.97	0.229	0.227	0.259	RANDOM	48.623

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]
-0.34			-0.07		0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.396
r_dihedral_angle_4_deg	19.968
r_dihedral_angle_3_deg	15.885
r_dihedral_angle_1_deg	6.086
r_scangle_it	2.111
r_scbond_it	1.322
r_angle_refined_deg	1.258
r_mcangle_it	0.836
r_mcbond_it	0.426
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.396
r_dihedral_angle_4_deg	19.968
r_dihedral_angle_3_deg	15.885
r_dihedral_angle_1_deg	6.086
r_scangle_it	2.111
r_scbond_it	1.322
r_angle_refined_deg	1.258
r_mcangle_it	0.836
r_mcbond_it	0.426
r_nbtor_refined	0.304
r_symmetry_vdw_refined	0.222
r_nbd_refined	0.199
r_xyhbond_nbd_refined	0.155
r_symmetry_hbond_refined	0.101
r_chiral_restr	0.085
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1769
Nucleic Acid Atoms
Solvent Atoms	42
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
d*TREK	data reduction
d*TREK	data scaling
SOLVE	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.