3GR5 | pdb_00003gr5

Periplasmic domain of the outer membrane secretin EscC from enteropathogenic E.coli (EPEC)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				microbatch, 2.0 M Ammonium sulfate + 0.1 M sodium acetate pH 4.5 or Bis-Tris pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
4.43	72.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.645	α = 90
b = 90.645	β = 90
c = 133.422	γ = 120

Symmetry
Space Group	P 65 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		CCD	ADSC QUANTUM 315			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1		ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.05	18.7	100				20942

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.05	18.7	20941	1072	99.79	0.215	0.213	0.2239	0.251	0.2326	RANDOM	42.164

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]
-0.23	-0.11		-0.23		0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	7.198
r_dihedral_angle_1_deg	6.576
r_scbond_it	4.355
r_mcangle_it	3.242
r_angle_refined_deg	2.102
r_mcbond_it	1.763
r_angle_other_deg	0.983
r_symmetry_vdw_refined	0.314
r_symmetry_vdw_other	0.314
r_symmetry_hbond_refined	0.293
r_nbd_other	0.251
r_nbd_refined	0.231
r_xyhbond_nbd_refined	0.171
r_chiral_restr	0.142
r_nbtor_other	0.092
r_bond_refined_d	0.032
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1237
Nucleic Acid Atoms
Solvent Atoms	77
Heterogen Atoms	15

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction