2Z8L | pdb_00002z8l

Crystal Structure of the Staphylococcal superantigen-like protein SSL5 at pH 4.6 complexed with sialyl Lewis X

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1M4V	PDB ENTRY 1M4V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	291	20% PEG 3350, 0.2M NaH2PO4, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.625	α = 90
b = 78.237	β = 127.02
c = 55.276	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	MARMOSAIC 325 mm CCD	mirror, monochromator	2006-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97892	SSRL	BL9-2

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	1.65	30.04	99.8	0.051	25.6	7.4	30728	30702

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	1.65	1.74	100		0.667	2.5	7.4	4497

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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 1M4V	1.65	28.05	30790	30702	1538	99.81	0.183	0.183	0.181	0.19	0.218	0.22	RANDOM	16.92

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]
0.31		0.37	-0.22		0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.736
r_dihedral_angle_4_deg	15.319
r_dihedral_angle_3_deg	13.459
r_dihedral_angle_1_deg	6.175
r_scangle_it	4.532
r_scbond_it	3.517
r_mcangle_it	2.093
r_mcbond_it	1.866
r_angle_refined_deg	1.744
r_angle_other_deg	0.91
r_mcbond_other	0.358
r_symmetry_vdw_other	0.236
r_nbd_refined	0.21
r_nbd_other	0.194
r_nbtor_refined	0.188
r_symmetry_vdw_refined	0.166
r_xyhbond_nbd_refined	0.153
r_symmetry_hbond_refined	0.143
r_chiral_restr	0.115
r_nbtor_other	0.094
r_bond_refined_d	0.018
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1607
Nucleic Acid Atoms
Solvent Atoms	111
Heterogen Atoms	67

Software

Software
Software Name	Purpose
MOSFLM	data reduction
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
SCALA	data scaling