3DCD | pdb_00003dcd

X-ray structure of the galactose mutarotase related enzyme Q5FKD7 from Lactobacillus acidophilus at the resolution 1.9A. Northeast Structural Genomics consortium target LaR33.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	277	0.1M KNO3, 0.1M Tris HCl, 24% PEG8K, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.27	α = 90
b = 88.27	β = 90
c = 139.54	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	CCD	MARMOSAIC 325 mm CCD		2008-05-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.979	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	1.9	50	99.5	0.072	30.2	14.2		99285		-3

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	1.9	1.97	95.2		0.219	9.2

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	SAD	THROUGHOUT	1.9	19.74	47985	2590	100	0.17936	0.17792	0.1773	0.20607	0.2046	RANDOM	19.783

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]
0.03			-0.06		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.262
r_dihedral_angle_4_deg	15.531
r_dihedral_angle_3_deg	11.884
r_dihedral_angle_1_deg	6.843
r_scangle_it	3.38
r_scbond_it	2.355
r_angle_refined_deg	1.302
r_mcangle_it	1.181
r_mcbond_it	0.845
r_nbtor_refined	0.306
r_nbd_refined	0.189
r_symmetry_vdw_refined	0.168
r_xyhbond_nbd_refined	0.122
r_symmetry_hbond_refined	0.111
r_chiral_restr	0.094
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4918
Nucleic Acid Atoms
Solvent Atoms	487
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SnB	phasing