3EO8 | pdb_00003eo8

Crystal structure of BluB-like flavoprotein (YP_001089088.1) from CLOSTRIDIUM DIFFICILE 630 at 1.74 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	277	15.0000% Glycerol, 0.1700M NH4OAc, 25.5000% PEG-4000, 0.1M Acetate pH 4.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.843	α = 90
b = 183.265	β = 104.89
c = 74.393	γ = 90

Symmetry
Space Group	P 1 21 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	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2008-08-04	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91837,0.97918,0.97934	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	1.74	48.337	97.8	0.12	8.64			133857		-3	14.167

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	1.74	1.8	96.8		0.711	1.9

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	1.74	48.337	133813	6747	97.86	0.159	0.156	0.17	0.198	0.2	RANDOM	27.441

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]
0.55		-1.2	-0.55		-0.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.76
r_dihedral_angle_4_deg	12.759
r_dihedral_angle_3_deg	12.347
r_dihedral_angle_1_deg	5.51
r_scangle_it	2.86
r_scbond_it	1.965
r_angle_refined_deg	1.334
r_mcangle_it	1.061
r_angle_other_deg	0.898
r_mcbond_it	0.767
r_symmetry_vdw_other	0.24
r_symmetry_vdw_refined	0.229
r_nbd_refined	0.225
r_mcbond_other	0.206
r_nbd_other	0.19
r_nbtor_refined	0.187
r_symmetry_hbond_refined	0.18
r_xyhbond_nbd_refined	0.155
r_nbtor_other	0.087
r_chiral_restr	0.081
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10336
Nucleic Acid Atoms
Solvent Atoms	2045
Heterogen Atoms	282

Software

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