1TKP | pdb_00001tkp

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

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	PEG400, 1 M 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	1.731	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	2.2	158	97.6	0.079	8.99	11		34572		2	18.9

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	PDB entry 1TJO	2.2	141.42	34572	1823	99.79	0.18792	0.18526	0.23758	RANDOM	46.409

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]
-1.1	-0.55		-1.1		1.65

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	7.615
r_dihedral_angle_1_deg	6.294
r_scbond_it	4.852
r_angle_refined_deg	2.506
r_mcangle_it	2.18
r_mcbond_it	1.169
r_nbd_refined	0.248
r_symmetry_vdw_refined	0.222
r_symmetry_hbond_refined	0.209
r_chiral_restr	0.187

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	7.615
r_dihedral_angle_1_deg	6.294
r_scbond_it	4.852
r_angle_refined_deg	2.506
r_mcangle_it	2.18
r_mcbond_it	1.169
r_nbd_refined	0.248
r_symmetry_vdw_refined	0.222
r_symmetry_hbond_refined	0.209
r_chiral_restr	0.187
r_xyhbond_nbd_refined	0.175
r_metal_ion_refined	0.075
r_bond_refined_d	0.034
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5459
Nucleic Acid Atoms
Solvent Atoms	227
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
ProDC	data collection
XDS	data scaling
MOLREP	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.