3SXE | pdb_00003sxe

Crystal structure of AAAA+UDP+Gal with Glycerol as the cryoprotectant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LZ0	PDB ENTRY 1LZ0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	HANGING DROP	7	298	1% PEG4000, 5% MPD, 100 mM ammonium sulfate, 70 mM sodium chloride, 50 mM ADA, pH 7.6, 30 mM sodium acetate, pH 4.6, 5 mM MnCl2, with 30% glycerol as the cryoprotectant, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.55	α = 90
b = 149.63	β = 90
c = 79.76	γ = 90

Symmetry
Space Group	C 2 2 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	IMAGE PLATE	RIGAKU RAXIS	OSMIC BLUE MIRRORS	2008-05-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-002	1.54

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	1.49	74.744	96.9	0.043	15.5	4.33		50161

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	1.49	1.54	97.8		0.364	3	3.53

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1LZ0	1.49	20	47595	2563	96.93	0.19173	0.19027	0.18	0.21938	0.21	RANDOM	21.006

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]
-0.45			0.18		0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.863
r_dihedral_angle_4_deg	16.882
r_dihedral_angle_3_deg	13.336
r_dihedral_angle_1_deg	6.499
r_scangle_it	5.089
r_scbond_it	3.383
r_mcangle_it	2.26
r_angle_refined_deg	2.256
r_mcbond_it	1.396
r_chiral_restr	0.158
r_bond_refined_d	0.029
r_gen_planes_refined	0.014
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2412
Nucleic Acid Atoms
Solvent Atoms	278
Heterogen Atoms	50

Software

Software
Software Name	Purpose
d*TREK	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data scaling
MOLREP	phasing