2YW7 | pdb_00002yw7

Crystal structure of C-terminal deletion mutant of Mycobacterium smegmatis Dps

X-RAY DIFFRACTION

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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	VAPOR DIFFUSION, HANGING DROP	8.5	293	30% PEG1140, 100mM CaCl2, 0.1M Tris-HCl pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.516	α = 90
b = 83.94	β = 105.89
c = 111.911	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	293	IMAGE PLATE	MAR scanner 300 mm plate		2006-01-20	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	3.3	30	100	0.0108	11.7	4.1		24653

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)
	3.3	3.382	100		0.0331	3.3		2467

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	3.3	28.54	24653	1320	100	0.22367	0.22179	0.2158	0.25878	0.2507	RANDOM	43.228

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]
		-0.02			-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.353
r_dihedral_angle_3_deg	19.755
r_dihedral_angle_4_deg	11.239
r_mcangle_it	6.052
r_mcbond_it	4.72
r_dihedral_angle_1_deg	4.363
r_scangle_it	2.34
r_scbond_it	1.36
r_angle_refined_deg	1.068
r_nbtor_refined	0.312
r_symmetry_vdw_refined	0.295
r_nbd_refined	0.26
r_metal_ion_refined	0.21
r_xyhbond_nbd_refined	0.161
r_chiral_restr	0.072
r_symmetry_hbond_refined	0.03
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11597
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing