5LQ8

1.52 A resolution structure of PhnD1 from Prochlorococcus marinus (MIT 9301) in complex with methylphosphonate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5LQ5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	290	0.1 M MMT (DL-malic acid, MES and Tris base) buffer pH 8.0 and 25% (w/v) PEG 1500

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.86	α = 90
b = 57.08	β = 106.56
c = 54.17	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 PILATUS 6M		2016-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.97951	Diamond	I24

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	1.52	44	97	0.021	0.997	16.2	2.2		40089

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	1.52	1.55	90.4		0.431	0.679	1.2	1.8

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	5LQ5	1.52	44	38156	1919	96.95	0.15997	0.15759	0.20707	RANDOM	37.022

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]
0.17		-2.46	1.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.696
r_sphericity_bonded	31.78
r_sphericity_free	20.86
r_dihedral_angle_4_deg	16.809
r_dihedral_angle_3_deg	14.46
r_scbond_other	11.302
r_scbond_it	11.294
r_scangle_other	10.552
r_rigid_bond_restr	10.184
r_long_range_B_other	8.912
r_long_range_B_refined	8.883
r_mcangle_other	7.974
r_mcangle_it	7.946
r_mcbond_it	7.577
r_mcbond_other	7.537
r_dihedral_angle_1_deg	6.15
r_angle_refined_deg	1.519
r_angle_other_deg	1.322
r_chiral_restr	0.092
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.003
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	2187
Nucleic Acid Atoms
Solvent Atoms	91
Heterogen Atoms	10

Software

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