2C5C | pdb_00002c5c

Shiga-like toxin 1 B subunit complexed with a bivalent inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		32% SATURATED AMMONIUM SULFATE, 2% MPD, 200 MM NACL, 100 MM HEPES [PH 6.5]

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.313	α = 90
b = 114.313	β = 90
c = 406.936	γ = 120

Symmetry
Space Group	H 3 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	MARRESEARCH	OSMIC	2002-09-27	M	SINGLE WAVELENGTH

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

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	2.86	24.04	91.5	0.18	6.8	3		196254		1.3

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	2.94	3.04	92.2		0.77	1.3	2.7

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 1QNU	2.94	22.76	19087	1029	90.4	0.201	0.198	0.2	0.267	0.28	RANDOM	33.44

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]
-0.01			-0.01		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.315
r_scangle_it	2.952
r_angle_refined_deg	2.479
r_scbond_it	1.795
r_angle_other_deg	1.174
r_mcangle_it	0.946
r_mcbond_it	0.49
r_symmetry_vdw_other	0.302
r_nbd_other	0.242
r_symmetry_hbond_refined	0.22
r_nbd_refined	0.209
r_xyhbond_nbd_refined	0.196
r_symmetry_vdw_refined	0.172
r_chiral_restr	0.129
r_nbtor_other	0.098
r_bond_refined_d	0.024
r_gen_planes_refined	0.008
r_gen_planes_other	0.006
r_bond_other_d	0.004
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5400
Nucleic Acid Atoms
Solvent Atoms	18
Heterogen Atoms	718

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing