3FNV | pdb_00003fnv

Crystal Structure of Miner1: The Redox-active 2Fe-2S Protein Causative in Wolfram Syndrome 2

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8	300	100 mM Tris-HCl pH 8.0, 100 mM NaCl, 15% PEG 3000, VAPOR DIFFUSION

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.904	α = 90
b = 48.579	β = 90
c = 74.104	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2008-12-15	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	1.7418, 1.3624, 1.7372	SSRL	BL9-2

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	1.8	48.56	98.6	0.143	16.17	25.9		14086		-3	34.594

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	1.8	1.86	97.9		1.79	1.9	17.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	2.1	37.06	9013	450	99.23	0.172	0.17	0.19	0.216	0.23	RANDOM	35.795

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]
0.11			-1.52		1.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.462
r_dihedral_angle_3_deg	11.835
r_dihedral_angle_4_deg	7.142
r_scangle_it	5.419
r_dihedral_angle_1_deg	4.144
r_scbond_it	4.088
r_mcangle_it	2.536
r_angle_refined_deg	1.859
r_mcbond_it	1.803
r_angle_other_deg	0.904
r_mcbond_other	0.5
r_symmetry_hbond_refined	0.306
r_nbd_refined	0.208
r_nbd_other	0.2
r_nbtor_refined	0.176
r_symmetry_vdw_refined	0.163
r_symmetry_vdw_other	0.143
r_xyhbond_nbd_refined	0.135
r_chiral_restr	0.098
r_nbtor_other	0.089
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1003
Nucleic Acid Atoms
Solvent Atoms	40
Heterogen Atoms	8

Software

Software
Software Name	Purpose
XSCALE	data scaling
SHARP	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
XDS	data reduction
SHELX	phasing