3BL9

Synthetic Gene Encoded DcpS bound to inhibitor DG157493

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ST0	PDB ENTRY 1ST0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		289	PEG 3350, Ammonium Formate, vapor diffusion, hanging drop, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.2	42.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.406	α = 62.35
b = 56.867	β = 77.93
c = 59.504	γ = 79.54

Symmetry
Space Group	P 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	RIGAKU SATURN 944	mirrors	2007-09-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.54178

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	1.8	50	91.6	0.052	20.8	4.6		47420

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)
	1.8	1.86	77.5		0.23		1.5	4029

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	PDB ENTRY 1ST0	1.8	33.13	47411	2418	91.55	0.176	0.174	0.222	RANDOM	17.248

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]
0.23	0.36	0.07	-0.13	0.2	-0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.983
r_dihedral_angle_4_deg	17.871
r_dihedral_angle_3_deg	13.144
r_dihedral_angle_1_deg	6.241
r_scangle_it	2.956
r_scbond_it	2.035
r_angle_refined_deg	1.394
r_mcangle_it	1.232
r_mcbond_it	1.089
r_angle_other_deg	0.918
r_symmetry_vdw_other	0.22
r_nbd_refined	0.211
r_symmetry_hbond_refined	0.207
r_nbd_other	0.204
r_mcbond_other	0.197
r_symmetry_vdw_refined	0.187
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.161
r_nbtor_other	0.084
r_chiral_restr	0.081
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4755
Nucleic Acid Atoms
Solvent Atoms	557
Heterogen Atoms	29

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
d*TREK	data scaling
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing