5BV3

Yeast Scavenger Decapping Enzyme in complex with m7GDP

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	100 mM Hepes, 100 mM NaCl, 1.6 M AmSO4

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.99	α = 90
b = 104.52	β = 90
c = 189.96	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	PIXEL	DECTRIS PILATUS 6M		2009-11-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.0	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.25	20	99.1	0.079	0.089	12.57	2.31		83079		-3	50.217

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.31	99.5		0.716	0.851	2.32

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1XMM	2.25	19.89	78749	4133	98.89	0.2228	0.2215	0.2481	RANDOM	54.795

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]
-5.37			1.63		3.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.862
r_dihedral_angle_4_deg	21.417
r_dihedral_angle_3_deg	13.843
r_dihedral_angle_1_deg	5.934
r_mcangle_it	4.207
r_mcbond_it	3.134
r_mcbond_other	3.134
r_angle_refined_deg	1.354
r_angle_other_deg	1.214
r_chiral_restr	0.076
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.006
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10329
Nucleic Acid Atoms
Solvent Atoms	146
Heterogen Atoms	97

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction