3SX5 | pdb_00003sx5

Crystal structure of AABB+UDP+Gal with MPD 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	1LZ7	PDB ENTRY 1LZ7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		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 manganese chloride, with 20% MPD as cryoprotectant, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.5	α = 90
b = 149.78	β = 90
c = 79.33	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	2007-11-09	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	1.43	74.953	95.6	0.031	20.7	4.24		55579

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	1.43	1.48	89.2		0.301	3.4	3.37	5096

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 1LZ7	1.43	20	55575	2801	95.63	0.2019	0.201	0.1918	0.2175	0.2085	RANDOM	20.3719

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]
-0.3			0.24		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.977
r_dihedral_angle_4_deg	18.835
r_dihedral_angle_3_deg	13.246
r_dihedral_angle_1_deg	6.672
r_scangle_it	5.226
r_scbond_it	3.568
r_angle_refined_deg	2.393
r_mcangle_it	2.257
r_mcbond_it	1.409
r_chiral_restr	0.166
r_bond_refined_d	0.03
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2355
Nucleic Acid Atoms
Solvent Atoms	258
Heterogen Atoms	45

Software

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