2HTD

CRYSTAL STRUCTURE OF A PUTATIVE PYRIDOXAMINE 5'-PHOSPHATE OXIDASE (LDB0262) FROM LACTOBACILLUS DELBRUECKII SUBSP. AT 1.60 A RESOLUTION

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4	277	2.4M (NH4)2SO4, 0.1M Citrate pH 4.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.89	34.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.104	α = 90
b = 71.123	β = 90.86
c = 47.031	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	2006-07-02	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91837,0.97929,0.97911	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.595	39.253	99.9	0.107	0.107	4.8	5.2		29681

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.68	99.8		0.987	0.987	0.7	3.6	4059

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.6	39.253	29659	1486	99.79	0.16	0.158	0.206	RANDOM	12.657

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]
-0.6		0.14	2.28		-1.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.097
r_dihedral_angle_4_deg	13.413
r_dihedral_angle_3_deg	12.389
r_scangle_it	6.49
r_dihedral_angle_1_deg	6.222
r_scbond_it	4.972
r_mcangle_it	2.788
r_mcbond_it	1.954
r_angle_refined_deg	1.566
r_angle_other_deg	0.873
r_mcbond_other	0.792
r_symmetry_vdw_refined	0.224
r_nbd_refined	0.216
r_symmetry_vdw_other	0.204
r_nbd_other	0.188
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.158
r_symmetry_hbond_refined	0.153
r_chiral_restr	0.088
r_nbtor_other	0.087
r_bond_refined_d	0.017
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	1874
Nucleic Acid Atoms
Solvent Atoms	205
Heterogen Atoms	31

Software

Software
Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
SHELXD	phasing
autoSHARP	phasing