7B53 | pdb_00007b53

Crystal structure of MurE from E.coli

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1E8C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	298	0.1M citrate pH 5.5 14% PEG4K 20% 2-propanol

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.631	α = 97.32
b = 58.944	β = 91.54
c = 74.228	γ = 105.17

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		2018-04-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	1.75	56.4	96.6	0.997	8.4	1.9		92515

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	1.75	1.8	93.5		0.495		1.3

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	1e8c	1.75	56.34	88075	4440	96.49	0.19645	0.19525	0.2	0.21971	0.23	RANDOM	38.196

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]
-0.98	0.96	-0.17	0.93	0.6	-0.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.743
r_dihedral_angle_4_deg	13.032
r_dihedral_angle_3_deg	12.508
r_long_range_B_refined	6.546
r_long_range_B_other	6.516
r_dihedral_angle_1_deg	5.351
r_scangle_other	4.542
r_scbond_it	3.099
r_scbond_other	3.099
r_mcangle_other	2.936
r_mcangle_it	2.935
r_mcbond_it	2.119
r_mcbond_other	2.117
r_angle_refined_deg	1.157
r_angle_other_deg	1.043
r_chiral_restr	0.067
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
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	424
Heterogen Atoms	16

Software

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