2QKM

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

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	285	8% Ethylene Glycol, 100 mM HEPES pH 7.0, 11.6% MPD, 4.4% PEG 4000 and 10 mM ATP, VAPOR DIFFUSION, HANGING DROP, temperature 285K

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.289	α = 90
b = 161.443	β = 97.49
c = 91.386	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	ADSC QUANTUM 315		2006-07-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.9792	ESRF	ID29

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	2.8	90.54	99.9	0.13		3.6	48289	48226	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	2.8	2.87	99.9		0.323	3.3	3.6

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entries 2A6T, 2QKL	2.8	20	48289	45695	2373	99.88	0.23611	0.23339	0.28923	RANDOM	57.918

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]
5.02		0.82	0.84		-5.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.251
r_dihedral_angle_3_deg	18.753
r_dihedral_angle_4_deg	17.63
r_dihedral_angle_1_deg	5.59
r_scangle_it	1.694
r_angle_refined_deg	1.241
r_mcangle_it	1.131
r_scbond_it	1.048
r_mcbond_it	0.633
r_nbtor_refined	0.312
r_symmetry_vdw_refined	0.26
r_nbd_refined	0.225
r_symmetry_hbond_refined	0.213
r_xyhbond_nbd_refined	0.158
r_chiral_restr	0.09
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11704
Nucleic Acid Atoms
Solvent Atoms	108
Heterogen Atoms	62

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASES	phasing