7B9W | pdb_00007b9w

Crystal structure of MurE from E.coli in complex with Z757284380

X-RAY DIFFRACTION

---

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 11.9% PEG4K 20.1% 2-propanol

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.409	α = 97.11
b = 58.621	β = 91.54
c = 74.438	γ = 104.841

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		2020-02-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.96862	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.78	56.36	97.57	0.074	0.088	0.048	0.998	8.9	3.3		88411

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.78	1.81	96.3		1.619	1.93	0.314	0.3	3.4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7B53	1.82	56.34	87246	4460	96.243	0.195	0.1929	0.2	0.2311	0.23	39.71

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]
-0.332	0.914	-0.362	0.592	0.244	-0.825

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.327
r_dihedral_angle_4_deg	19.045
r_dihedral_angle_3_deg	14.018
r_lrange_it	8.596
r_lrange_other	8.587
r_scangle_it	6.702
r_scangle_other	6.701
r_dihedral_angle_1_deg	6.528
r_mcangle_it	4.576
r_mcangle_other	4.575
r_scbond_it	4.277
r_scbond_other	4.276
r_mcbond_it	3.17
r_mcbond_other	3.16
r_angle_refined_deg	1.505
r_angle_other_deg	1.317
r_symmetry_nbd_refined	0.241
r_nbd_other	0.206
r_nbd_refined	0.205
r_symmetry_nbd_other	0.173
r_xyhbond_nbd_refined	0.161
r_symmetry_xyhbond_nbd_refined	0.158
r_nbtor_refined	0.152
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.068
r_symmetry_xyhbond_nbd_other	0.012
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	303
Heterogen Atoms	27

Software

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