4F6T | pdb_00004f6t

The crystal structure of the molybdenum storage protein (MoSto) from Azotobacter vinelandii loaded with various polyoxometalates

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OGX	PDB entry 2OGX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	277	NH4H2PO4, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
2	VAPOR DIFFUSION, SITTING DROP	5.6	283	NH4H2PO4, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 283K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.74	α = 90
b = 115.74	β = 90
c = 233.62	γ = 120

Symmetry
Space Group	P 63 2 2

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 225 mm CCD		2009-03-03	M	SINGLE WAVELENGTH
2	2	x-ray	100	CCD	ADSC QUANTUM 315r		2010-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.008	SLS	X10SA
2	SYNCHROTRON	ESRF BEAMLINE ID29	1.71	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	1.6	46	90	0.085	13.45	4.4	121767	109553		-3	22.705

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)
1,2	1.6	1.7	59.4		0.548	3.61

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 2OGX	1.6	46	-3	121767	109551	5467	89.99	0.1421	0.1421	0.1394	0.14	0.1733	0.17	RANDOM	22.3128

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]
-0.09	-0.05		-0.09		0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.965
r_dihedral_angle_4_deg	16.84
r_dihedral_angle_3_deg	13.894
r_scangle_it	8.005
r_dihedral_angle_1_deg	6.185
r_angle_refined_deg	5.8
r_scbond_it	5.727
r_mcangle_it	3.927
r_rigid_bond_restr	3.047
r_mcbond_it	2.668

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.965
r_dihedral_angle_4_deg	16.84
r_dihedral_angle_3_deg	13.894
r_scangle_it	8.005
r_dihedral_angle_1_deg	6.185
r_angle_refined_deg	5.8
r_scbond_it	5.727
r_mcangle_it	3.927
r_rigid_bond_restr	3.047
r_mcbond_it	2.668
r_chiral_restr	0.322
r_bond_refined_d	0.031
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3800
Nucleic Acid Atoms
Solvent Atoms	524
Heterogen Atoms	172

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
EDNA	data collection
XDS	data reduction
REFMAC	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.