5UH0 | pdb_00005uh0

1.95 Angstrom Resolution Crystal Structure of Fragment (35-274) of Membrane-bound Lytic Murein Transglycosylase F from Yersinia pestis.

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4OWD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	295	Protein: 17.3 mg/ml, 0.01M Tris HCl (pH 8.3); Screen: JCSG+ (H8), 0.2M Sodium chloride, 0.1 Bis-Tris (pH 5.5), 25% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
1.88	34.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.086	α = 90
b = 66.507	β = 90
c = 96.427	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD	C(111)	2016-04-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rpim I (All)	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	30	100	0.11	0.11	0.045	29.5	7.2		30781		-3	27.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	1.98	100		0.7	0.7	0.277	0.895	3.2	7.3

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	4OWD	1.95	29.52	29200	1513	99.9	0.216	0.21327	0.22	0.26735	0.27	RANDOM	35.574

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]
1.78			-2.23		0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.49
r_dihedral_angle_4_deg	12.493
r_dihedral_angle_3_deg	11.58
r_long_range_B_refined	6.952
r_long_range_B_other	6.894
r_scangle_other	5.114
r_mcangle_other	3.529
r_mcangle_it	3.528
r_dihedral_angle_1_deg	3.446
r_scbond_it	3.391
r_scbond_other	3.39
r_mcbond_it	2.449
r_mcbond_other	2.443
r_angle_refined_deg	1.504
r_angle_other_deg	0.87
r_chiral_restr	0.095
r_gen_planes_refined	0.023
r_gen_planes_other	0.02
r_bond_refined_d	0.012
r_bond_other_d	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	3658
Nucleic Acid Atoms
Solvent Atoms	198
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing