2ISY | pdb_00002isy

Crystal structure of the nickel-activated two-domain iron-dependent regulator (IdeR)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FX7	PDB entry 1FX7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.2	298	0.6 M Na/K phosphate pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.954	α = 110.18
b = 44.743	β = 96.57
c = 49.641	γ = 108.29

Symmetry
Space Group	P 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			2003-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	1.03320	APS	19-ID

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	1.95	50	91.8	0.06	12.6			20610

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)
	1.95	2.02	58.1		0.173			1293

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 1FX7	1.955	45.13	20606	1058	91.51	0.178	0.176	0.18	0.211	0.21	RANDOM	28.607

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]
2.04	0.1	-0.6	-1.04	-1.29	-1.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.51
r_dihedral_angle_4_deg	23.683
r_dihedral_angle_3_deg	16.53
r_dihedral_angle_1_deg	5.046
r_scangle_it	3.688
r_scbond_it	2.651
r_mcangle_it	2.629
r_mcbond_it	1.695
r_angle_refined_deg	1.282
r_nbtor_refined	0.315

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.51
r_dihedral_angle_4_deg	23.683
r_dihedral_angle_3_deg	16.53
r_dihedral_angle_1_deg	5.046
r_scangle_it	3.688
r_scbond_it	2.651
r_mcangle_it	2.629
r_mcbond_it	1.695
r_angle_refined_deg	1.282
r_nbtor_refined	0.315
r_symmetry_vdw_refined	0.284
r_nbd_refined	0.234
r_xyhbond_nbd_refined	0.209
r_symmetry_hbond_refined	0.174
r_chiral_restr	0.097
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_metal_ion_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2359
Nucleic Acid Atoms
Solvent Atoms	148
Heterogen Atoms	14

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

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.