3BPC

co-crystal structure of S25-2 Fab in complex with 5-deoxy-4-epi-2,3-dehydro Kdo (4.8) Kdo

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8		PEG 4000, ethelyene glycol, pH 8.0, VAPOR DIFFUSION

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.85	α = 90
b = 81.29	β = 90
c = 132.34	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		IMAGE PLATE	RIGAKU RAXIS		2007-01-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.54

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	1.8	19.97	94.5	0.073	9	3.49		44150

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)
	1.8	1.86	99.5		0.228	4	3.73	4550

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.85	20	40510	2071	94.01	0.226	0.224	0.273	RANDOM	22.304

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]
1			-0.8		-0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.15
r_dihedral_angle_4_deg	20.431
r_dihedral_angle_3_deg	14.208
r_dihedral_angle_1_deg	7.12
r_scangle_it	3.656
r_scbond_it	2.629
r_angle_refined_deg	1.723
r_mcangle_it	1.571
r_mcbond_it	1.002
r_symmetry_metal_ion_refined	0.428
r_nbtor_refined	0.302
r_xyhbond_nbd_refined	0.284
r_symmetry_vdw_refined	0.245
r_nbd_refined	0.222
r_symmetry_hbond_refined	0.14
r_chiral_restr	0.123
r_metal_ion_refined	0.095
r_bond_refined_d	0.018
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3315
Nucleic Acid Atoms
Solvent Atoms	461
Heterogen Atoms	36

Software

Software
Software Name	Purpose
d*TREK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction