3BL7 | pdb_00003bl7

Synthetic Gene Encoded DcpS bound to inhibitor DG156844

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, SITTING DROP		289	PEG 3350, Ammonium Formate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.257	α = 118.81
b = 56.271	β = 92.39
c = 60.334	γ = 99.99

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	2007-06-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	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	2.31	50	96.2	0.123	7.2	2		23402	1	1

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)
	2.31	2.39	94.4		0.43		2	2293

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	PDB entry 1ST0	2.31	28.95	22214	1184	96.05	0.21404	0.21071	0.22	0.27605	0.23	RANDOM	16.827

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]
0.5	-0.06	0.21	-0.14	-0.29	-0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.606
r_dihedral_angle_4_deg	19.17
r_dihedral_angle_3_deg	16.436
r_dihedral_angle_1_deg	6.167
r_scangle_it	1.524
r_angle_refined_deg	1.21
r_scbond_it	0.983
r_angle_other_deg	0.877
r_mcangle_it	0.675
r_mcbond_it	0.594
r_symmetry_vdw_other	0.211
r_xyhbond_nbd_refined	0.198
r_nbd_refined	0.195
r_nbd_other	0.194
r_symmetry_vdw_refined	0.178
r_symmetry_hbond_refined	0.176
r_nbtor_refined	0.171
r_nbtor_other	0.082
r_mcbond_other	0.068
r_chiral_restr	0.067
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4759
Nucleic Acid Atoms
Solvent Atoms	211
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing