9FLK | pdb_00009flk

Crystal structure of the C-terminal domain of VldE from Streptococcus pneumoniae containing two zinc atoms at the binding site

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	291	100 mM TRIS-HCL, pH 8.5, 50 mM CADMIUM SULFATE, 1 M SODIUM ACETATE

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.121	α = 90
b = 59.121	β = 90
c = 32.676	γ = 120

Symmetry
Space Group	P 3

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		2019-09-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	1.28	ALBA	XALOC

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	1.85	32.68	94.8	0.151	0.151	8.9	9.7		10367			21.7

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	1.85	1.85	100		1.308	1.308	1.3	10

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	SPR1875 C-TERMINAL DOMAIN	1.85	15	10346	470	94.6	0.213	0.2179	0.258	0.2563	34.56

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]
0.31	0.155		0.31		-1.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.257
r_dihedral_angle_4_deg	30.184
r_dihedral_angle_3_deg	15.968
r_dihedral_angle_1_deg	6.723
r_scangle_it	5.799
r_scangle_other	5.798
r_mcangle_it	4.706
r_mcangle_other	4.703
r_scbond_it	4.324
r_scbond_other	4.252
r_mcbond_it	3.151
r_mcbond_other	3.141
r_angle_refined_deg	1.672
r_angle_other_deg	1.287
r_xyhbond_nbd_refined	0.2
r_nbd_refined	0.184
r_nbtor_refined	0.16
r_nbd_other	0.115
r_metal_ion_refined	0.099
r_chiral_restr	0.072
r_symmetry_metal_ion_refined	0.038
r_bond_refined_d	0.021
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_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	862
Nucleic Acid Atoms
Solvent Atoms	100
Heterogen Atoms	4

Software

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