Experiment: 6RYP

Bacterial membrane enzyme structure by the in meso method at 2.3 A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6RYO	model from D_1292102692

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE		293	100 mM MES/NaOH pH 6.5, 40 %(v/v) PEG400, 400 mM ammonium fluoride and 80 mM magnesium sulfate

Crystal Properties
Matthews coefficient	Solvent content
3.64	66.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.17	α = 90
b = 54.17	β = 90
c = 317.54	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 EIGER X 16M		2017-11-25	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	2.3	46.4	99.9	0.14	0.99	7.69	7.69		23038

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.36	100		2.79	0.22	0.9	8.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	model from D_1292102692	2.3	46.4	1.33	23038	1129	99.73	0.2557	0.2545	0.2755	0.2811	0.2673

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	8.66
f_angle_d	0.372
f_chiral_restr	0.038
f_plane_restr	0.002
f_bond_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1284
Nucleic Acid Atoms
Solvent Atoms	12
Heterogen Atoms	220

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data scaling
XSCALE	data scaling
PHASER	phasing
XDS	data reduction