2KMB | pdb_00002kmb

COMPLEX OF 3'-NEUAC-LEWIS-X WITH A SELECTIN-LIKE MUTANT OF MANNOSE-BINDING PROTEIN A

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.8		8-10% PEG 8000, 2% PEG 1000, 1 MM TRIS-CL, PH 7.8, 200 MM NACL, 20 MM CACL2, 2 MM NAN3. PRIOR TO DATA COLLECTION, THE CRYSTAL WAS ADAPTED TO THE MOTHER LIQUOR PLUS 20% MPD PLUS 80 MM 3'-NEUAC-LEWIS-X.

Crystal Properties
Matthews coefficient	Solvent content
3.2	68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.1	α = 90
b = 85	β = 107.1
c = 98.8	γ = 90

Symmetry
Space Group	C 1 2 1

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 IIC	COLLIMATOR	1996-04-05	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH2R

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2	40	98.6	0.06	0.06	10.6	2.4		41761		-3	19.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.07	93.2		0.264	0.264	3.7	2.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1RTM	2	10	2	38875	3872	92.7	0.19	0.19	0.19	0.247	RANDOM	22.2

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]
6.8		5.22	0.12		7.77

RMS Deviations
Key	Refinement Restraint Deviation
x_dihedral_angle_d	21.9
x_scangle_it	5.7
x_mcangle_it	3.7
x_scbond_it	2.9
x_mcbond_it	1.9
x_angle_deg	1.2
x_improper_angle_d	1.2
x_bond_d	0.007
x_bond_d_na
x_bond_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3477
Nucleic Acid Atoms
Solvent Atoms	458
Heterogen Atoms	183

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.