5UPQ | pdb_00005upq

Acyl-CoA synthetase PtmA2 from Streptomyces platensis in complex with SBNP465 ligand

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5E7Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	289	0.1 M Bis Tris Propane buffer, 1.5 M lithium chloride

Crystal Properties
Matthews coefficient	Solvent content
3.25	62.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.608	α = 90
b = 145.737	β = 90
c = 145.756	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	CCD	ADSC QUANTUM 315r		2015-10-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9792	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	2.42	38.5	99.7	0.123	0.133	0.05	8.3	7.1		57650

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.42	2.46	99.5		0.909	0.982	0.368	0.617	2.2	7

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	5E7Q	2.42	38.5	54772	2820	99.36	0.2341	0.2315	0.2331	0.2846	0.2846	RANDOM	46.854

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]
0.54			-0.64		0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.395
r_dihedral_angle_4_deg	15.114
r_dihedral_angle_3_deg	14.629
r_dihedral_angle_1_deg	5.992
r_angle_refined_deg	1.351
r_angle_other_deg	0.786
r_chiral_restr	0.072
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7662
Nucleic Acid Atoms
Solvent Atoms	212
Heterogen Atoms	166

Software

Software
Software Name	Purpose
HKL-3000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing
DENZO	data reduction
SCALEPACK	data scaling