1TJO | pdb_00001tjo

Iron-oxo clusters biomineralizing on protein surfaces. Structural analysis of H.salinarum DpsA in its low and high iron states

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DPS	Dps-protein from E. coli - PDB entry 1DPS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	PEG400, 1M NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.1	42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.11	α = 90
b = 91.11	β = 90
c = 150.04	γ = 120

Symmetry
Space Group	P 3 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	CCD	ADSC QUANTUM 4		2003-09-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.93	ESRF	ID29

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	1.6	158	96.5	0.074	10	5.5		92251		2	28.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.641	99.1

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Dps-protein from E. coli - PDB entry 1DPS	1.6	15	87268	6766	98.53	0.16808	0.16484	0.21039	RANDOM	21.515

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]
-0.33	-0.17		-0.33		0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	6.308
r_dihedral_angle_1_deg	4.862
r_scbond_it	3.806
r_mcangle_it	1.895
r_angle_refined_deg	1.509
r_mcbond_it	0.952
r_angle_other_deg	0.934
r_symmetry_vdw_other	0.306
r_symmetry_hbond_refined	0.269
r_xyhbond_nbd_refined	0.265
r_nbd_other	0.26
r_nbd_refined	0.255
r_symmetry_vdw_refined	0.202
r_chiral_restr	0.125
r_nbtor_other	0.09
r_metal_ion_refined	0.044
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_gen_planes_other	0.005
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5459
Nucleic Acid Atoms
Solvent Atoms	796
Heterogen Atoms	22

Software

Software
Software Name	Purpose
REFMAC	refinement
ProDC	data collection
XDS	data scaling
AMoRE	phasing