4ERR | pdb_00004err

1.55 Angstrom Crystal Structure of the Four Helical Bundle Membrane Localization Domain (4HBM) of the Vibrio vulnificus MARTX Effector Domain DUF5

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2EBF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	295	Protein: 13mG/mL, 0.1M Sodium chloride, TRIS-HCl pH 7.0, 6.9 mM Phosphatidylserine (PS); Screen: JCSG+ (G10), 0.15M Potassium bromide, 30% w/v PEG MME 2000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.896	α = 90
b = 49.874	β = 90
c = 72.102	γ = 90

Symmetry
Space Group	P 21 21 21

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	Beryllium lenses	2012-02-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	1.55	30	99.6	0.054	26.7	6	24039	24039		-3	28.7

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	1.55	1.58	99.4		0.555	3.1	5.3	1175

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	MOLECULAR REPLACEMENT	THROUGHOUT	2EBF	1.55	29.22	22766	22766	1223	99.38	0.16983	0.16983	0.16717	0.17	0.2152	0.21	RANDOM	23.373

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]
-0.5			1.19		-0.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.114
r_dihedral_angle_3_deg	13.26
r_dihedral_angle_4_deg	10.595
r_scangle_it	6.532
r_scbond_it	4.42
r_dihedral_angle_1_deg	3.671
r_mcangle_it	3.268
r_mcbond_it	1.97
r_angle_refined_deg	1.187
r_rigid_bond_restr	1.063

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.114
r_dihedral_angle_3_deg	13.26
r_dihedral_angle_4_deg	10.595
r_scangle_it	6.532
r_scbond_it	4.42
r_dihedral_angle_1_deg	3.671
r_mcangle_it	3.268
r_mcbond_it	1.97
r_angle_refined_deg	1.187
r_rigid_bond_restr	1.063
r_angle_other_deg	0.852
r_mcbond_other	0.828
r_chiral_restr	0.075
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1285
Nucleic Acid Atoms
Solvent Atoms	239
Heterogen Atoms	4

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.