1TKO | pdb_00001tko

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	1MOJ	PDB entry 1MOJ

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	MARRESEARCH		2003-09-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.731	SLS	X06SA

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	2.9	15	94.2	0.093	9.75	3.8		15444		2	61.5

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 1MOJ	2.9	15	15444	1183	97.73	0.18396	0.17782	0.26281	RANDOM	58.447

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]
-2.66	-1.33		-2.66		3.99

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	10.469
r_dihedral_angle_1_deg	7.941
r_scbond_it	6.265
r_angle_refined_deg	4.378
r_mcangle_it	3.169
r_mcbond_it	1.518
r_nbd_refined	0.321
r_symmetry_vdw_refined	0.294
r_chiral_restr	0.258
r_xyhbond_nbd_refined	0.209

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	10.469
r_dihedral_angle_1_deg	7.941
r_scbond_it	6.265
r_angle_refined_deg	4.378
r_mcangle_it	3.169
r_mcbond_it	1.518
r_nbd_refined	0.321
r_symmetry_vdw_refined	0.294
r_chiral_restr	0.258
r_xyhbond_nbd_refined	0.209
r_symmetry_hbond_refined	0.171
r_metal_ion_refined	0.148
r_bond_refined_d	0.06
r_gen_planes_refined	0.015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5459
Nucleic Acid Atoms
Solvent Atoms	40
Heterogen Atoms	50

Software

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