5MGY | pdb_00005mgy

Crystal structure of Pseudomonas stutzeri flavinyl transferase ApbE, apo form

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	281	0.1 M Bis-Tris pH 6.5 28% polyethylene glycol 2000 monomethyl ether

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.656	α = 90
b = 91.983	β = 90.41
c = 138.061	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	PIXEL	DECTRIS PILATUS 2M-F		2015-08-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.6	138.06	100	2.7	6.9		104767

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		THROUGHOUT	2.6	138.06	99638	5134	99.95	0.23392	0.23187	0.2327	0.27394	0.2706	RANDOM	60.044

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]
1.11		0.75	-1.24		0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.159
r_dihedral_angle_4_deg	18.353
r_dihedral_angle_3_deg	16.932
r_long_range_B_refined	12.314
r_long_range_B_other	12.314
r_dihedral_angle_1_deg	6.624
r_scangle_other	6.451
r_mcangle_it	6.406
r_mcangle_other	6.406
r_mcbond_it	3.937
r_mcbond_other	3.937
r_scbond_it	3.883
r_scbond_other	3.883
r_angle_refined_deg	2.004
r_angle_other_deg	1.12
r_chiral_restr	0.1
r_bond_refined_d	0.018
r_gen_planes_refined	0.009
r_bond_other_d	0.004
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	18672
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement