7PL5

Crystal structure of choline-binding module (R1-R9) of LytB from Streptococcus pneumoniae

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2V05

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291.15	MES buffer Zinc sulfate PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.41	49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.299	α = 90
b = 96.143	β = 100.966
c = 49.096	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	PIXEL	DECTRIS PILATUS 6M		2017-03-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.979260	ALBA	XALOC

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	1.99	48.2	98.7	0.238	0.108	6	5.5		28181

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	1.99	2.03			0.952	0.496

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2V05	1.99	44.504	28134	1439	99.245	0.175	0.1723	0.2328	25.524

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]
0.866		1.014	-0.332		-0.862

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.769
r_dihedral_angle_4_deg	34.099
r_dihedral_angle_3_deg	17.074
r_lrange_it	7.704
r_lrange_other	7.7
r_dihedral_angle_1_deg	7.298
r_scangle_it	5.998
r_scangle_other	5.996
r_mcangle_it	4.202
r_mcangle_other	4.202
r_scbond_it	3.98
r_scbond_other	3.979
r_mcbond_it	2.983
r_mcbond_other	2.974
r_angle_refined_deg	1.827
r_angle_other_deg	1.512
r_nbd_other	0.293
r_nbd_refined	0.207
r_symmetry_nbd_other	0.2
r_symmetry_nbd_refined	0.196
r_nbtor_refined	0.195
r_symmetry_xyhbond_nbd_refined	0.173
r_xyhbond_nbd_refined	0.165
r_symmetry_metal_ion_refined	0.121
r_ncsr_local_group_1	0.108
r_symmetry_nbtor_other	0.09
r_chiral_restr	0.089
r_symmetry_xyhbond_nbd_other	0.072
r_metal_ion_refined	0.049
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3029
Nucleic Acid Atoms
Solvent Atoms	212
Heterogen Atoms	98

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MoRDa	phasing