9FLN | pdb_00009fln

Crystal structure of the C-terminal domain of VldE H373A from Streptococcus pneumoniae

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	7.2	291	100 mM Hepes pH 7.2, 50 mM Cadmium sulfate and 0.6 M Sodium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.139	α = 90
b = 59.139	β = 90
c = 32.481	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		2023-06-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.979	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.14	29.57	100	0.052	0.057	0.999	18.8	9.9		46365

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.14	1.16	100		1.879	0.401	1.1	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-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	1.14	29.569	46362	2404	99.985	0.109	0.1074	0.1352	0.1278	0.1494	18.184

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]
-8.187			-8.187		16.374

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.406
r_dihedral_angle_3_deg	11.658
r_dihedral_angle_2_deg	10.838
r_lrange_it	7.579
r_lrange_other	6.352
r_dihedral_angle_1_deg	5.833
r_scangle_it	2.73
r_scangle_other	2.728
r_mcangle_it	2.661
r_mcangle_other	2.661
r_mcbond_it	1.737
r_scbond_it	1.729
r_mcbond_other	1.727
r_scbond_other	1.721
r_rigid_bond_restr	1.075
r_angle_refined_deg	0.979
r_angle_other_deg	0.358
r_symmetry_nbd_refined	0.25
r_symmetry_xyhbond_nbd_refined	0.211
r_nbd_refined	0.199
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.176
r_nbd_other	0.161
r_xyhbond_nbd_refined	0.145
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.048
r_bond_refined_d	0.003
r_gen_planes_refined	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	889
Nucleic Acid Atoms
Solvent Atoms	136
Heterogen Atoms	3

Software

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