9FLH | pdb_00009flh

Crystal structure of the C-terminal domain of VldE from Streptococcus pneumoniae containing four 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	7.5	291	100 mM HEPES, pH 7.5, 50 mM CADMIUM SULFATE, 1 M SODIUM ACETATE

Crystal Properties
Matthews coefficient	Solvent content
2.16	42.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.861	α = 90
b = 56.861	β = 90
c = 32.334	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 PILATUS3 6M		2015-07-08	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	1.5	49.24	100	0.036	0.036	0.998	9.8		18745			25.74

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	1.5	1.55	100		1.335	1.335	0.809	9.5

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	1.5	32.36	18745	963	100	0.196	0.2016	0.242	0.2504	31.64

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]
-1.09	-0.545		-1.09		3.537

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.135
r_dihedral_angle_4_deg	21.19
r_dihedral_angle_3_deg	16.606
r_dihedral_angle_1_deg	6.13
r_scangle_it	5.25
r_scangle_other	5.246
r_mcangle_it	4.009
r_mcangle_other	4.006
r_scbond_it	3.95
r_scbond_other	3.946
r_angle_refined_deg	2.726
r_mcbond_other	2.552
r_mcbond_it	2.548
r_angle_other_deg	1.466
r_xyhbond_nbd_refined	0.264
r_nbd_refined	0.242
r_symmetry_metal_ion_refined	0.241
r_nbd_other	0.188
r_nbtor_refined	0.179
r_metal_ion_refined	0.106
r_chiral_restr	0.071
r_bond_refined_d	0.03
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.001
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	845
Nucleic Acid Atoms
Solvent Atoms	67
Heterogen Atoms	14

Software

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