5FQU

Orthorhombic crystal structure of of PlpD (selenomethionine derivative)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				20%W/V PEG3350, 200MM SODIUM NITRATE, 0.6% N-DODECYL-BETA-D MALTOSIDE

Crystal Properties
Matthews coefficient	Solvent content
2.6	53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.743	α = 90
b = 113.393	β = 90
c = 130.416	γ = 90

Symmetry
Space Group	P 21 21 21

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 6M		2013-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29		ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.74	85.58	99.5	0.01	10.42	4.5		19015		2.8	46.511

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.74	2.9	96.5		0.54	2.81	4.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	NONE	2.74	85.57	17914	968	99.31	0.19805	0.19579	0.23801	RANDOM	69.713

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]
-9.82			18.06		-8.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.121
r_dihedral_angle_4_deg	20.308
r_dihedral_angle_3_deg	13.91
r_mcangle_it	9.451
r_scbond_it	8.194
r_dihedral_angle_1_deg	6.941
r_mcbond_it	6.596
r_mcbond_other	6.576
r_angle_refined_deg	1.416
r_angle_other_deg	0.866
r_chiral_restr	0.077
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_gen_planes_other	0.004
r_bond_other_d	0.003
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3702
Nucleic Acid Atoms
Solvent Atoms	61
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
autoSHARP	phasing