5LQ1

1.41 A resolution structure of PtxB from Trichodesmium erythraeum IMS101 in complex with methylphosphonate

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	290	0.2 M Magnesium chloride, 0.1 M Sodium acetate pH 5.0 and 20 % (w/v) PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.481	α = 84.82
b = 53.703	β = 78.26
c = 66.388	γ = 69.74

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	PIXEL	DECTRIS PILATUS 6M		2016-07-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97629	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	1.41	65.05	95.2	0.032	0.999	9.1	3.3		91920

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	1.41	1.43	75.4		0.664	0.48	1.1	2.8

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5JVB	1.41	64.98	86075	4350	93.66	0.18221	0.1798	0.23031	RANDOM	26.361

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]
0.92	0.69	-0.29	0.15	-0.18	-0.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.506
r_sphericity_bonded	31.373
r_sphericity_free	20.522
r_dihedral_angle_4_deg	18.193
r_dihedral_angle_3_deg	12.98
r_scbond_it	9.544
r_scbond_other	9.544
r_rigid_bond_restr	8.723
r_scangle_other	8.096
r_long_range_B_refined	6.458
r_long_range_B_other	6.458
r_dihedral_angle_1_deg	5.876
r_mcangle_other	4.089
r_mcangle_it	4.088
r_mcbond_it	3.891
r_mcbond_other	3.891
r_angle_refined_deg	1.514
r_angle_other_deg	1.109
r_chiral_restr	0.091
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.002
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3998
Nucleic Acid Atoms
Solvent Atoms	213
Heterogen Atoms	18

Software

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