5MT6

Structure of E.coli GlpG in complex with peptide derived inhibitor Ac-RVRHA-phenylethyl-ketoamide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2XOV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	295	2M sodium chloride

Crystal Properties
Matthews coefficient	Solvent content
3.5	64.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.71	α = 90
b = 111.71	β = 90
c = 124.229	γ = 120

Symmetry
Space Group	H 3 2

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-F		2015-11-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.9794	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.16	52.31	99.4	0.08	10.2	4.7		16097

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	2.16	2.23	99.6		0.72	0.559	1.9	4.6

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	2XOV	2.16	52.31	15315	781	99.32	0.21598	0.21355	0.22	0.26593	0.27	RANDOM	47.458

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]
-0.35	-0.18		-0.35		1.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.811
r_long_range_B_refined	12.753
r_long_range_B_other	12.748
r_dihedral_angle_3_deg	12.716
r_scangle_other	11.056
r_dihedral_angle_4_deg	9.941
r_scbond_it	9.273
r_scbond_other	9.267
r_mcangle_it	7.296
r_mcangle_other	7.296
r_mcbond_it	6.951
r_mcbond_other	6.943
r_dihedral_angle_1_deg	6.019
r_angle_refined_deg	1.508
r_angle_other_deg	0.948
r_chiral_restr	0.082
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	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	1478
Nucleic Acid Atoms
Solvent Atoms	28
Heterogen Atoms	22

Software

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