9FLM | pdb_00009flm

Crystal structure of the C-terminal domain of VldE from Streptococcus pneumoniae in a catalytically competent conformation

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

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 and 1 M of Sodium acetate, soaked with 20 mM EDTA

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.111	α = 90
b = 57.111	β = 90
c = 32.674	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		2023-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.9793	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	28.56	99.3	0.223	0.109	0.986	6.1	10.2		18946

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.53	99.1		1.759	0.864	0.715	1.3	10.2

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-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.5	28.556	18928	912	99.131	0.167	0.1655	0.1626	0.1987	0.1962	29.239

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]
-15.593			-15.593		31.187

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.822
r_dihedral_angle_3_deg	12.987
r_dihedral_angle_2_deg	6.965
r_dihedral_angle_1_deg	6.257
r_lrange_it	5.502
r_lrange_other	5.173
r_mcangle_it	2.175
r_mcangle_other	2.173
r_scangle_it	1.755
r_scangle_other	1.754
r_mcbond_it	1.298
r_mcbond_other	1.292
r_scbond_it	1.044
r_scbond_other	1.042
r_angle_refined_deg	1.008
r_angle_other_deg	0.379
r_symmetry_xyhbond_nbd_refined	0.294
r_symmetry_nbd_refined	0.271
r_symmetry_metal_ion_refined	0.27
r_xyhbond_nbd_refined	0.206
r_symmetry_nbd_other	0.199
r_nbd_refined	0.187
r_nbtor_refined	0.176
r_nbd_other	0.133
r_symmetry_nbtor_other	0.074
r_symmetry_xyhbond_nbd_other	0.053
r_chiral_restr	0.05
r_metal_ion_refined	0.027
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	894
Nucleic Acid Atoms
Solvent Atoms	133
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing