6SIW | pdb_00006siw

PaaK family AMP-ligase with AMP

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.2 M KSCN, 0.1 M sodium citrate pH 6.0, 30% PEG MME 2K

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.131	α = 90
b = 138.094	β = 90
c = 130.426	γ = 90

Symmetry
Space Group	C 2 2 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-F		2018-03-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	1.0056	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.96	84.65	99.9	0.108	0.999	12.8	10.7		69487

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.96	1.99	98.8		0.901	0.522		10

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	1.96	84.65	65021	3574	98.68	0.2014	0.1995	0.2121	0.2364	0.2462	RANDOM	41.282

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]
-3.2			3.14		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.13
r_dihedral_angle_4_deg	19.391
r_dihedral_angle_3_deg	14.21
r_dihedral_angle_1_deg	7.045
r_angle_refined_deg	1.416
r_angle_other_deg	1.239
r_chiral_restr	0.066
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6752
Nucleic Acid Atoms
Solvent Atoms	261
Heterogen Atoms	117

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data scaling
PDB_EXTRACT	data extraction
xia2	data reduction
SHARP	phasing