1ZS3

The crystal structure of the Lactococcus lactis MG1363 DpsB protein

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QGH	PDB entry 1qgh

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	298	2.0M Sodium Formate, 0.1M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.74	57.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.977	α = 90
b = 128.379	β = 90
c = 193.903	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	298	CCD	ADSC QUANTUM 4	Mirrors	2001-05-11	M	SINGLE WAVELENGTH
2	1	x-ray	298	CCD	ADSC QUANTUM 4	Mirrors	2001-06-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX14.2	0.98	SRS	PX14.2
2	SYNCHROTRON	SRS BEAMLINE PX14.2	0.98	SRS	PX14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.7	15	97.8	0.074	0.074	7.5	3.2	85912	85912			61.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.7	2.85	97.4		0.407	0.407	1.7	3.2	12388

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1qgh	2.7	15	77125	77125	4108	92.31	0.2094	0.20941	0.20683	0.25779	RANDOM	44.165

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]
-0.14			0.18		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.715
r_scangle_it	3.378
r_scbond_it	1.906
r_angle_refined_deg	1.692
r_mcangle_it	1.66
r_angle_other_deg	1.59
r_mcbond_it	0.882
r_symmetry_vdw_other	0.308
r_symmetry_vdw_refined	0.299
r_symmetry_hbond_refined	0.269
r_nbd_other	0.237
r_nbd_refined	0.234
r_xyhbond_nbd_refined	0.192
r_chiral_restr	0.098
r_nbtor_other	0.097
r_gen_planes_other	0.05
r_bond_other_d	0.043
r_gen_planes_refined	0.025
r_bond_refined_d	0.022
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16644
Nucleic Acid Atoms
Solvent Atoms	131
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
CCP4	phasing