2I7F

Sphingomonas yanoikuyae B1 ferredoxin

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	288	0.05M phosphate buffer, 0.1M citric acid, 1.6M ammonium sulfate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 288K

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.064	α = 90
b = 62.064	β = 90
c = 238.436	γ = 120

Symmetry
Space Group	P 65 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			2004-02-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A	1.03320	NSLS	X6A

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	1.62	49	70.4	0.125	8.1	4.74	25261	25261

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)
	1.62	1.68	7.2		0.539	1.2	1.24	254

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1FQT	1.9	9.5	20863	20863	1059	93.28	0.196	0.196	0.193	0.24	RANDOM	15.189

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]
1.26	0.63		1.26		-1.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.69
r_dihedral_angle_3_deg	14.525
r_dihedral_angle_1_deg	7.364
r_dihedral_angle_4_deg	4.678
r_scangle_it	3.357
r_scbond_it	2.464
r_angle_refined_deg	1.935
r_mcangle_it	1.314
r_mcbond_it	1.061
r_angle_other_deg	0.972
r_symmetry_hbond_refined	0.354
r_symmetry_vdw_refined	0.346
r_mcbond_other	0.233
r_symmetry_vdw_other	0.222
r_xyhbond_nbd_refined	0.209
r_nbd_refined	0.202
r_nbd_other	0.188
r_nbtor_refined	0.179
r_chiral_restr	0.102
r_nbtor_other	0.088
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_metal_ion_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	1547
Nucleic Acid Atoms
Solvent Atoms	193
Heterogen Atoms	39

Software

Software
Software Name	Purpose
d*TREK	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
d*TREK	data reduction