3LM1 | pdb_00003lm1

Crystal Structure Analysis of Maclura pomifera agglutinin complex with p-nitrophenyl-GalNAc

X-RAY DIFFRACTION

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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	0.5M of lithium sulfate, 12% PEG 8000, 1% octyl-beta-D-glucopyranoside, 0.1M Hepes, pH 7.0 in the reservoir solution. The sitting drop is made by protein (28mg/mL) and equal volumn of reservoir solution in the presence of p-nitrophenyl-alpha-GalNAc., VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.53	65.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.09	α = 90
b = 133.29	β = 90
c = 200.05	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	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	1.9	29.8	83.8	0.039	24.7	3	145978	122330	2	2	36.7

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)
	1.9	1.97	46.6		0.29	4.5	2.1	6716

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-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 1JOT	2.1	20	2	108366	99067	9650	91.4	0.244	0.223	0.223	0.2182	0.244	0.2519	random	26.595

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]
2.508			-0.445		-2.064

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	2.622
c_scbond_it	1.804
c_mcangle_it	1.76
c_mcbond_it	1.143

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9263
Nucleic Acid Atoms
Solvent Atoms	879
Heterogen Atoms	168

Software

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