5OVT

Thiobacillus denitrificans BPH in complex with Epoxomicin

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		294	100 mM sodium acetate pH 4.8, 1.2 M sodium nitrate

Crystal Properties
Matthews coefficient	Solvent content
5.11	75.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 196.82	α = 90
b = 196.82	β = 90
c = 296.37	γ = 120

Symmetry
Space Group	P 61 2 2

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		2015-09-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1	SLS	X10SA

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	2.95	39.2	99.9	0.439	0.995	13.6	57.1		71632

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	2.95	3.12	100		1.98	0.878	3.11	57.6

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.95	39.2	68023	3609	99.8	0.17323	0.17242	0.1886	RANDOM	41.589

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]
-0.34	-0.17		-0.34		1.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.89
r_dihedral_angle_4_deg	18.403
r_dihedral_angle_3_deg	15.661
r_long_range_B_other	7.539
r_long_range_B_refined	7.538
r_dihedral_angle_1_deg	6.595
r_scangle_other	5.414
r_scbond_it	4.214
r_scbond_other	4.073
r_mcangle_it	3.871
r_mcangle_other	3.871
r_mcbond_it	2.738
r_mcbond_other	2.738
r_angle_refined_deg	2.111
r_angle_other_deg	1.173
r_chiral_restr	0.107
r_bond_refined_d	0.02
r_gen_planes_refined	0.011
r_bond_other_d	0.008
r_gen_planes_other	0.007
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10073
Nucleic Acid Atoms
Solvent Atoms	79
Heterogen Atoms	35

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
SHELXDE	phasing