3EFP | pdb_00003efp

Crystal structure of the Escherichia coli twin arginine leader peptide binding protein DmsD in a monomeric form

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1S9U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	1.25M ammonium sulfate, 12% glycerol, 0.1M Bis-Tris pH 6.5, 72 hours, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.9	68.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.02	α = 90
b = 128.02	β = 90
c = 78.723	γ = 120

Symmetry
Space Group	P 31 2 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	IMAGE PLATE	RIGAKU RAXIS IV++	Rigaku VariMAX HF	2007-08-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	2.01	30.75	97.7	0.089		5.72	49796	48639	2	2	92.8

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	2.01	2.08	95.6		0.362	4.5	5.58	4703

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		THROUGHOUT	1s9u	2.01	30.75	49796	48639	2463	97.7	0.236	0.18	0.178	0.1795	0.213	0.2117	RANDOM	22.692

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]
0.43	0.22		0.43		-0.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.863
r_dihedral_angle_4_deg	18.4
r_dihedral_angle_3_deg	12.736
r_dihedral_angle_1_deg	4.644
r_scangle_it	1.583
r_angle_refined_deg	1.036
r_scbond_it	1.02
r_mcangle_it	0.554
r_nbtor_refined	0.316
r_mcbond_it	0.312

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.863
r_dihedral_angle_4_deg	18.4
r_dihedral_angle_3_deg	12.736
r_dihedral_angle_1_deg	4.644
r_scangle_it	1.583
r_angle_refined_deg	1.036
r_scbond_it	1.02
r_mcangle_it	0.554
r_nbtor_refined	0.316
r_mcbond_it	0.312
r_symmetry_hbond_refined	0.244
r_symmetry_vdw_refined	0.231
r_nbd_refined	0.208
r_xyhbond_nbd_refined	0.196
r_chiral_restr	0.073
r_bond_refined_d	0.007
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3345
Nucleic Acid Atoms
Solvent Atoms	411
Heterogen Atoms	75

Software

Software
Software Name	Purpose
d*TREK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction
PHASER	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.