3C6S | pdb_00003c6s

Crystal structure of Fab F22-4 in complex with a Shigella flexneri 2a O-Ag pentadecasaccharide

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3C5S	pdb entry 3C5S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.6	290	25% PEG 5000 MME, 0.2M Li2SO4, 0.1M Tris, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.86	α = 90
b = 137.15	β = 94.97
c = 109.38	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	ADSC QUANTUM 4	bent mirror	2006-06-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.933	ESRF	ID14-2

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	1.8	45.74	99.2	0.112	0.112	5	3.8	179612	179612	-3	-3	16.86

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	1.8	1.9	97.5		0.668	0.668	1	3.5	25673

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 3C5S	1.8	44.79	176903	176903	2670	99.11	0.1923	0.1923	0.19141	0.2	0.25109	0.25	RANDOM	18.781

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]
-0.68		-0.02	2.2		-1.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.102
r_dihedral_angle_4_deg	16.002
r_dihedral_angle_3_deg	14.173
r_dihedral_angle_1_deg	6.876
r_scangle_it	2.715
r_scbond_it	2.004
r_mcangle_it	1.957
r_angle_refined_deg	1.626
r_mcbond_it	1.578
r_angle_other_deg	0.804
r_mcbond_other	0.322
r_symmetry_hbond_refined	0.28
r_symmetry_vdw_refined	0.257
r_nbd_refined	0.199
r_xyhbond_nbd_refined	0.198
r_nbd_other	0.196
r_symmetry_vdw_other	0.196
r_nbtor_refined	0.181
r_symmetry_hbond_other	0.151
r_chiral_restr	0.091
r_nbtor_other	0.087
r_xyhbond_nbd_other	0.018
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13125
Nucleic Acid Atoms
Solvent Atoms	2124
Heterogen Atoms	481

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
XDS	data reduction
SCALA	data scaling
PHASER	phasing