6B8D | pdb_00006b8d

1.78 Angstrom Resolution Crystal Structure of N-terminal Fragment (residues 1-405) of Elongation Factor G from Haemophilus influenzae

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5TV2	PDB entry 5TV2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	295	11.0 mg/mL protein in 0.5 M sodium chloride, 0.01 M Tris-HCl, pH 8.3 against screen: Classics II (F6), 0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 5.5, 25% w/v PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.823	α = 90
b = 88.487	β = 90
c = 130.279	γ = 90

Symmetry
Space Group	C 2 2 21

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)	2017-08-08	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	1.78	30	99.9	0.043	0.043	0.018	38.4	6.9		47575		-3	32.7

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	1.78	1.81	100		0.797	0.797	0.325	0.832	2.6	6.9

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 5TV2	1.78	29.8	44829	2357	99.84	0.17457	0.17257	0.18	0.21366	0.22	RANDOM	43.177

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]
0.75			0.83		-1.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.006
r_dihedral_angle_4_deg	9.541
r_dihedral_angle_3_deg	8.898
r_long_range_B_refined	5.598
r_long_range_B_other	5.389
r_dihedral_angle_1_deg	2.988
r_scangle_other	2.515
r_mcangle_it	1.987
r_mcangle_other	1.986
r_scbond_it	1.532
r_scbond_other	1.532
r_angle_refined_deg	1.368
r_mcbond_it	1.234
r_mcbond_other	1.232
r_angle_other_deg	0.864
r_chiral_restr	0.088
r_gen_planes_refined	0.022
r_gen_planes_other	0.019
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	2941
Nucleic Acid Atoms
Solvent Atoms	290
Heterogen Atoms	1

Software

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