5VRV | pdb_00005vrv

2.05 Angstrom Resolution Crystal Structure of C-terminal Domain (DUF2156) of Putative Lysylphosphatidylglycerol Synthetase from Agrobacterium fabrum.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295	Protein: 70.0 mg/ml, 0.01M HEPES (pH 7.5), Screen: 0.2M Potassium citrate, 0.3M 3-(1-Pyridinio)-1-propanesulfonate, 20% (w/v) P3350 20%

Crystal Properties
Matthews coefficient	Solvent content
2.46	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 194.403	α = 90
b = 194.403	β = 90
c = 50.228	γ = 120

Symmetry
Space Group	P 32

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD	C(111)	2017-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rpim I (All)	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	2.05	30	100	0.084	0.084	0.039	20.4	5.6		133171		-3	33.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.09	100		0.775	0.775	0.38	0.694	2.2	5.1

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.05	29.65	126438	6697	99.94	0.19161	0.18964	0.2	0.22818	0.23	RANDOM	42.957

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]
0.53	0.27		0.53		-1.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.234
r_dihedral_angle_4_deg	10.145
r_dihedral_angle_3_deg	9.424
r_long_range_B_refined	4.91
r_long_range_B_other	4.858
r_scangle_other	3.157
r_mcangle_it	2.324
r_mcangle_other	2.324
r_dihedral_angle_1_deg	2.288
r_scbond_it	2.016
r_scbond_other	2.015
r_mcbond_it	1.499
r_mcbond_other	1.498
r_angle_refined_deg	1.429
r_angle_other_deg	0.881
r_chiral_restr	0.083
r_gen_planes_refined	0.022
r_gen_planes_other	0.018
r_bond_refined_d	0.009
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14802
Nucleic Acid Atoms
Solvent Atoms	669
Heterogen Atoms	29

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing