Experiment: 3LLZ

Crystal Structure Analysis of Maclura pomifera agglutinin complex with Gal-beta-1,3-GalNAc

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	0.5 M of lithium sulfate, 12% PEG 8000, 1% octyl-beta-D-glucopyranoside, 0.1M Hepes, pH 7.0 in the resevoir solution. the sitting drop is made by protein (28mg/mL) and equal volumn of reservoir solution in the presence of Gal-beta-1,3-GalNAc., VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.54	α = 90
b = 66.54	β = 90
c = 147.95	γ = 120

Symmetry
Space Group	P 64 2 2

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	ADSC QUANTUM 4r	mirrors	2000-06-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A	0.9793	NSLS	X4A

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	1.5	26.3	98.2	0.052	35	8.1	31933	31358	2	2	23.36

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)
	1.5	1.55	86.6		0.199	6.8	4.7	2693

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 1JOT	1.55	20	2	28958	27054	2175	93.4	0.222	0.21	0.2185	0.227	0.2351	random	19.407

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]
-3.343	-1.908		-3.343		6.686

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	2.963
c_scbond_it	2.02
c_mcangle_it	1.608
c_mcbond_it	1.097

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1151
Nucleic Acid Atoms
Solvent Atoms	155
Heterogen Atoms	26

Software

Software
Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
APEX	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing