6BK7 | pdb_00006bk7

1.83 Angstrom Resolution Crystal Structure of N-terminal Fragment (residues 1-404) of Elongation Factor G from Enterococcus faecalis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5VH6	PDB entry 5VH6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.3	295	12.5 mg/mL protein in 0.5 sodium chloride, 0.01 M Tris, pH 8.3 against screen PEGs II (G6), 15% w/v PEG6000, 5% w/v glycerol, cryoprotectant: reservoir

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.45	α = 90
b = 86.425	β = 90.17
c = 75.442	γ = 90

Symmetry
Space Group	P 1 21 1

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)	2017-11-02	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)	Rrim I (All)	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	1.83	30	99.8	0.046	0.046	0.052	0.025	28.8	4.5		69321		-3	35.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.83	1.86	99.5		0.793	0.793	0.9	0.423	0.774	2.05	4.4

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-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 5VH6	1.83	28.95	65859	3436	99.66	0.19278	0.19145	0.2	0.21734	0.22	RANDOM	48.832

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]
-1.19		-0.42	-1.65		2.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.788
r_dihedral_angle_4_deg	13.115
r_dihedral_angle_3_deg	9.891
r_long_range_B_refined	5.183
r_long_range_B_other	5.151
r_scangle_other	2.984
r_dihedral_angle_1_deg	2.873
r_mcangle_it	2.393
r_mcangle_other	2.393
r_scbond_it	1.859
r_scbond_other	1.858
r_mcbond_it	1.523
r_mcbond_other	1.522
r_angle_refined_deg	1.371
r_angle_other_deg	0.829
r_chiral_restr	0.084
r_gen_planes_refined	0.021
r_gen_planes_other	0.018
r_bond_refined_d	0.008
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	5950
Nucleic Acid Atoms
Solvent Atoms	378
Heterogen Atoms	2

Software

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