2QOM | pdb_00002qom

The crystal structure of the E.coli EspP autotransporter Beta-domain.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		from MAD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.4	294	0.34M Cymal-1, 1% octylglucoside, 33% PEG 1000, 0.2M NaCl, 0.1M Na cacodylate pH 6.4, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
3.6	65.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.951	α = 90
b = 53.298	β = 103.57
c = 102.418	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	CCD	MARMOSAIC 300 mm CCD		2006-07-01	M	MAD
2	1	x-ray	100	CCD	MAR CCD 225 mm		2006-08-22	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.97180, 0.97925, 0.97947	APS	22-ID
2	SYNCHROTRON	APS BEAMLINE 22-BM	0.97121	APS	22-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.66	50	96.7	0.105	13	6.4	23299	23299

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	2.66	2.76	79.4		0.553	1.92	5.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MAD folllowed by Molecular Replacement	THROUGHOUT	from MAD	2.66	15	23299	23299	1243	95.44	0.25959	0.25959	0.25825	0.3	0.28424	0.33	RANDOM	53.36

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]
-8.44		1.8	11.84		-2.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.128
r_dihedral_angle_3_deg	17.287
r_dihedral_angle_4_deg	14.722
r_dihedral_angle_1_deg	8.632
r_scangle_it	4.321
r_scbond_it	3.546
r_mcangle_it	3.441
r_mcbond_it	2.32
r_angle_refined_deg	1.286
r_angle_other_deg	0.929
r_mcbond_other	0.798
r_symmetry_vdw_other	0.292
r_symmetry_vdw_refined	0.254
r_nbd_other	0.192
r_nbtor_refined	0.19
r_nbd_refined	0.179
r_xyhbond_nbd_refined	0.14
r_chiral_restr	0.124
r_nbtor_other	0.087
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4011
Nucleic Acid Atoms
Solvent Atoms	6
Heterogen Atoms

Software

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