2BKC | pdb_00002bkc

The X-ray structure of the H43G Listeria innocua Dps mutant

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				PEG 100 15-30% W/V, ACETATE BUFFERS AT PH VALUES BETWEEN 5.5-6.5

Crystal Properties
Matthews coefficient	Solvent content
2.63	40.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.726	α = 90
b = 175.648	β = 92.53
c = 135.957	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	100	CCD	MARRESEARCH			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R		ELETTRA	5.2R

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	2.3	50	91.5	0.08	10	2		172339

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	2.3	2.38	89.7		0.3	5	2

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	PDB ENTRY 1QGH	2.3	25	163334	8690	91.5	0.212	0.209	0.21	0.266	0.27	RANDOM	29.08

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]
1.25		-0.55	0.3		-1.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.888
r_scangle_it	3.667
r_scbond_it	2.216
r_angle_refined_deg	1.593
r_mcangle_it	1.255
r_angle_other_deg	0.908
r_mcbond_it	0.639
r_nbd_other	0.233
r_symmetry_vdw_refined	0.226
r_nbd_refined	0.214
r_symmetry_vdw_other	0.201
r_xyhbond_nbd_refined	0.191
r_chiral_restr	0.102
r_nbtor_other	0.094
r_symmetry_hbond_refined	0.068
r_bond_refined_d	0.018
r_gen_planes_refined	0.006
r_gen_planes_other	0.004
r_bond_other_d	0.002
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	29174
Nucleic Acid Atoms
Solvent Atoms	182
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing