7B6J

Crystal structure of MurE from E.coli in complex with minifrag succinimide

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 11.6% PEG4K 18.4% 2-propanol

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.258	α = 96.824
b = 58.291	β = 91.36
c = 74.633	γ = 104.993

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		2019-10-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.95	47.61	99.7	0.1	0.998	10.2	6.6		68240

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	1.95	2	96.7		0.823	0.599	1.2	3.6

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7B53	2.09	47.61	68208	3496	99.534	0.186	0.183	0.2361	41.526

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]
-0.159	2.354	0.502	0.721	0.994	-2.208

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.682
r_dihedral_angle_4_deg	15.557
r_dihedral_angle_3_deg	13.866
r_lrange_it	7.229
r_lrange_other	7.229
r_dihedral_angle_1_deg	6.831
r_scangle_it	5.936
r_scangle_other	5.936
r_mcangle_it	4.22
r_mcangle_other	4.22
r_scbond_it	3.952
r_scbond_other	3.951
r_mcbond_it	3.059
r_mcbond_other	3.056
r_angle_refined_deg	1.487
r_angle_other_deg	1.331
r_symmetry_xyhbond_nbd_refined	0.341
r_nbd_refined	0.205
r_nbd_other	0.205
r_xyhbond_nbd_refined	0.194
r_symmetry_nbd_other	0.175
r_symmetry_xyhbond_nbd_other	0.158
r_nbtor_refined	0.152
r_symmetry_nbd_refined	0.133
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.068
r_xyhbond_nbd_other	0.013
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7282
Nucleic Acid Atoms
Solvent Atoms	320
Heterogen Atoms	37

Software

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