6SLA

Crystal structure of isomerase PaaG mutant - D136N with Oxepin-CoA

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		297	50 mM KH2PO4, pH 4.5, 20-22% PEG 3350, 3% (w/v) NDSB-201 and 20% glycerol (v/v)

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.156	α = 90
b = 73.05	β = 92.482
c = 130.304	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS EIGER X 16M		2018-09-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.55	48.645	96.84	0.997	9.82	6.8		45527

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.55	2.641			0.2727

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3HRX	2.55	48.645	45463	2301	96.849	0.203	0.2008	0.2523	54.132

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]
1.753		0.423	0.459		-2.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.865
r_dihedral_angle_4_deg	21.395
r_dihedral_angle_3_deg	18.276
r_lrange_it	11.723
r_scangle_it	9.304
r_mcangle_it	7.253
r_scbond_it	6.69
r_dihedral_angle_1_deg	6.593
r_mcbond_it	5.149
r_angle_refined_deg	1.585
r_nbtor_refined	0.308
r_symmetry_nbd_refined	0.29
r_symmetry_xyhbond_nbd_refined	0.263
r_nbd_refined	0.231
r_xyhbond_nbd_refined	0.162
r_chiral_restr	0.121
r_ncsr_local_group_1	0.099
r_ncsr_local_group_2	0.098
r_ncsr_local_group_15	0.096
r_ncsr_local_group_4	0.094
r_ncsr_local_group_9	0.094
r_ncsr_local_group_12	0.094
r_ncsr_local_group_11	0.093
r_ncsr_local_group_3	0.092
r_ncsr_local_group_6	0.092
r_ncsr_local_group_14	0.092
r_ncsr_local_group_8	0.09
r_ncsr_local_group_10	0.09
r_ncsr_local_group_13	0.088
r_ncsr_local_group_7	0.085
r_ncsr_local_group_5	0.082
r_bond_refined_d	0.01
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11166
Nucleic Acid Atoms
Solvent Atoms	64
Heterogen Atoms	348

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing