9FLJ | pdb_00009flj

Crystal structure of the C-terminal domain of VldE from Streptococcus pneumoniae containing three 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, 5 MM EDTA

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.192	α = 90
b = 57.192	β = 90
c = 32.506	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		2019-03-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	1.2837	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	1.6	28.6	99.7	0.144	0.144	7.4	8.9		15644			26.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.63	100		0.381	0.8	9.8

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	C-TERMINAL DOMAIN OF SPR1875 CONTAINING FOUR ZINC ATOMS	1.6	28.6	15643	741	99.7	0.218	0.2195	0.254	0.2461	30.17

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]
-12.39			-12.39		24.779

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.289
r_dihedral_angle_4_deg	19.001
r_dihedral_angle_3_deg	15.008
r_dihedral_angle_1_deg	6.566
r_scangle_it	3.459
r_scangle_other	3.456
r_mcangle_it	3.288
r_mcangle_other	3.286
r_scbond_it	2.748
r_scbond_other	2.674
r_mcbond_it	2.194
r_mcbond_other	2.187
r_angle_refined_deg	1.76
r_angle_other_deg	1.2
r_nbd_refined	0.187
r_nbtor_refined	0.17
r_xyhbond_nbd_refined	0.156
r_nbd_other	0.133
r_chiral_restr	0.062
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbtor_other
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_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	851
Nucleic Acid Atoms
Solvent Atoms	76
Heterogen Atoms	9

Software

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