7B60 | pdb_00007b60

Crystal structure of MurE from E.coli in complex with Z1269139261

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7B53

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	294	0.1M citrate pH 5.5 17% PEG4K 16% 2-propanol

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.249	α = 97.27
b = 58.382	β = 91.53
c = 74.027	γ = 105.61

Symmetry
Space Group	P 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	PIXEL	DECTRIS PILATUS3 S 6M		2018-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91587	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	1.91	73.28	95.4	0.999	8.8	1.8		68830

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.91	2.01			0.436

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	7B53	1.91	73.28	65319	3511	95.39	0.21741	0.21608	0.22	0.24193	0.24	RANDOM	51.58

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]
0.14	1.12	-0.22	0.33	1.02	-1.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.243
r_dihedral_angle_4_deg	15.649
r_dihedral_angle_3_deg	12.77
r_long_range_B_refined	5.797
r_long_range_B_other	5.795
r_dihedral_angle_1_deg	5.407
r_scangle_other	3.763
r_mcangle_it	3.322
r_mcangle_other	3.31
r_scbond_it	2.345
r_scbond_other	2.345
r_mcbond_it	2.084
r_mcbond_other	2.084
r_angle_refined_deg	1.038
r_angle_other_deg	0.979
r_chiral_restr	0.057
r_bond_refined_d	0.006
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7284
Nucleic Acid Atoms
Solvent Atoms	206
Heterogen Atoms	58

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing