5NWP | pdb_00005nwp

Crystal Structure of the Lectin Domain From the F17-like Adhesin, UclD

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Se-SAD model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	16% PEG 4000, 0.1M Tris HCl pH 8.5, 0.2M MgCl2

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.089	α = 90
b = 91.871	β = 96.46
c = 64.932	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	100	CCD	ADSC QUANTUM 315r		2010-01-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.008	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	1.05	91.87	88.8	0.079	0.034	11.9	5		144393			5.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.05	1.11	43.8		0.336	0.308	2.1	2

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	Se-SAD model	1.05	91.87	137073	7242	88.7	0.11839	0.11711	0.13	0.14252	0.15	RANDOM	11.786

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]
0.09		-0.08	-0.15		0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.311
r_sphericity_free	28.643
r_dihedral_angle_4_deg	23.326
r_sphericity_bonded	10.845
r_dihedral_angle_3_deg	10.302
r_dihedral_angle_1_deg	7.467
r_rigid_bond_restr	7.128
r_long_range_B_refined	5.417
r_scangle_other	4.791
r_long_range_B_other	4.721
r_scbond_it	3.914
r_scbond_other	3.913
r_mcangle_other	2.268
r_mcangle_it	2.266
r_angle_refined_deg	2.232
r_mcbond_it	1.917
r_mcbond_other	1.913
r_angle_other_deg	1.417
r_chiral_restr	0.148
r_bond_refined_d	0.027
r_gen_planes_refined	0.012
r_gen_planes_other	0.008
r_bond_other_d	0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2914
Nucleic Acid Atoms
Solvent Atoms	646
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
SHELXD	phasing