2YW6 | pdb_00002yw6

Structural studies of N terminal deletion mutant of Dps from Mycobacterium smegmatis

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Microbath under oil	8	293	protein buffer in 50mM Tris-HCl (pH8.0), 0.2M Calcium chloride, 0.1M HEPES-Na pH7.5, 28% polyethelene glycol 400, Microbath under oil, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.93	36.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.443	α = 90
b = 87.443	β = 90
c = 212.537	γ = 120

Symmetry
Space Group	P 62 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	100	IMAGE PLATE	MAR scanner 300 mm plate		2005-10-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	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	2.53	30	94.4	0.098	28	17		15936			45.1

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	2.53	2.69	88.3		0.497	3.83		1411

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1VEI	2.53	28.62	15897	776	94.4	0.229	0.229	0.23	0.246	0.25	RANDOM	46.6

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]
-1.14	0.58		3.78		-2.64

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	19
c_scangle_it	6.78
c_mcangle_it	5.46
c_scbond_it	4.12
c_mcbond_it	3.31
c_angle_deg	1.2
c_improper_angle_d	0.77
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3555
Nucleic Acid Atoms
Solvent Atoms	185
Heterogen Atoms

Software

Software
Software Name	Purpose
CNS	refinement
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	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.