Experiment: 6WM6

Periplasmic EDTA-binding protein EppA, tetragonal

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VR5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	297	100 mM Tris, 2.0 M ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.805	α = 90
b = 87.805	β = 90
c = 164.484	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	PIXEL	DECTRIS PILATUS 6M		2018-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1	ALS	5.0.2

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	1.416	41.1	97.4	0.16	0.996	10.57	20		122095			20.01

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	1.416	1.467			0.8602	0.887	4.77

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1vr5	1.42	41.1	119276	1939	97.33	0.1442	0.1441	0.145	0.1525	0.1522	26.13

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	15.9916
f_angle_d	0.9422
f_chiral_restr	0.0781
f_plane_restr	0.0075
f_bond_d	0.0073

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4128
Nucleic Acid Atoms
Solvent Atoms	599
Heterogen Atoms	43

Software

Software
Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
PHENIX	refinement