2J1V | pdb_00002j1v

Structure of a Streptococcus pneumoniae fucose binding module in complex with the blood group H-trisaccharide

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	20-22% polyethylene glycol 1500, 0.15M KSCN, and 0.1M Tris-HCl, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
1.64	24.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.827	α = 90
b = 60.465	β = 90
c = 99.498	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	113					M	SINGLE WAVELENGTH

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

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	1.45	20	99.6	0.065	13.8	6.4		45077		2

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	1.45	1.5	99.5		0.384	4.2	6.4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.45	51.99	45077	2397	99.6	0.154	0.152	0.17	0.208	0.17	RANDOM	12.62

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]
-0.32			0.56		-0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.401
r_scangle_it	4.532
r_scbond_it	3.079
r_mcangle_it	2.162
r_angle_refined_deg	1.629
r_mcbond_it	1.438
r_angle_other_deg	0.965
r_symmetry_vdw_refined	0.289
r_symmetry_vdw_other	0.289
r_nbd_other	0.263
r_nbd_refined	0.241
r_xyhbond_nbd_refined	0.216
r_symmetry_hbond_refined	0.202
r_chiral_restr	0.111
r_nbtor_other	0.084
r_gen_planes_other	0.021
r_bond_refined_d	0.016
r_gen_planes_refined	0.013
r_bond_other_d	0.003
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	2198
Nucleic Acid Atoms
Solvent Atoms	624
Heterogen Atoms	38

Software

Software
Software Name	Purpose
REFMAC	refinement
MOLREP	phasing