6N0I | pdb_00006n0i

2.60 Angstrom Resolution Crystal Structure of Elongation Factor G 2 from Pseudomonas putida.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4FN5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	292	Protein: 9.5 mg/ml, 0.01M Tris HCl (pH 8.3); Screen: PACT (C10), 0.2M Magnesium chloride, 0.1M HEPES (pH 7.0), 20% (w/v) PEG 6000.

Crystal Properties
Matthews coefficient	Solvent content
2.41	49.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.434	α = 90
b = 79.968	β = 94.21
c = 183.516	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)	2017-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	2.6	30	100	0.078	0.078	0.041	17.3	4.4		44241		-3	65.9

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	2.6	2.64	100		0.804	0.804	0.912	0.427	0.742	1.9	4.5

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	4FN5	2.6	29.83	41967	2120	99.91	0.22517	0.22316	0.22	0.26393	0.26	RANDOM	71.367

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]
-2.06		1.04	4.46		-2.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	12.598
r_dihedral_angle_4_deg	7.327
r_long_range_B_refined	7.091
r_long_range_B_other	7.084
r_dihedral_angle_3_deg	6.857
r_scangle_other	4.425
r_mcangle_it	4.034
r_mcangle_other	4.034
r_scbond_it	2.708
r_scbond_other	2.708
r_mcbond_it	2.426
r_mcbond_other	2.425
r_dihedral_angle_1_deg	1.478
r_angle_refined_deg	1.168
r_angle_other_deg	0.292
r_gen_planes_refined	0.053
r_chiral_restr	0.049
r_gen_planes_other	0.049
r_bond_refined_d	0.003
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	10509
Nucleic Acid Atoms
Solvent Atoms	116
Heterogen Atoms	17

Software

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