3IN6 | pdb_00003in6

Crystal structure of a fmn-binding protein (swol_0183) from syntrophomonas wolfei subsp. wolfei at 2.12 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.29	277	30.5000% 2-methyl-2,4-pentanediol, 0.1M sodium acetate pH 4.29, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.108	α = 90
b = 103.108	β = 90
c = 59.786	γ = 90

Symmetry
Space Group	P 42 21 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 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2009-03-20	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91162,0.97936,0.97922	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	2.12	28.712	99.5	0.057	16.01	7.12		18788		-3	35.044

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	2.12	2.2	99.5		0.554	2.5

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	2.12	28.712	18752	958	99.54	0.221	0.219	0.22	0.254	0.25	RANDOM	29.909

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]
-2.9			-2.9		5.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.961
r_dihedral_angle_4_deg	15.427
r_dihedral_angle_3_deg	11.289
r_scangle_it	6.174
r_scbond_it	4.443
r_dihedral_angle_1_deg	3.483
r_mcangle_it	2.359
r_angle_refined_deg	1.431
r_mcbond_it	1.301
r_angle_other_deg	0.842

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.961
r_dihedral_angle_4_deg	15.427
r_dihedral_angle_3_deg	11.289
r_scangle_it	6.174
r_scbond_it	4.443
r_dihedral_angle_1_deg	3.483
r_mcangle_it	2.359
r_angle_refined_deg	1.431
r_mcbond_it	1.301
r_angle_other_deg	0.842
r_mcbond_other	0.342
r_chiral_restr	0.079
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2290
Nucleic Acid Atoms
Solvent Atoms	41
Heterogen Atoms	70

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHARP	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.