8BKE

Crystal structure of the Klebsiella phage KP34p57 capsular depolymerase

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.4	293	0.04 M cytric acid, 0.06 M bis-tris propane, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.34	α = 90
b = 140.985	β = 102.633
c = 81.925	γ = 90

Symmetry
Space Group	P 1 21 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 2M		2021-02-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.987	ESRF	BM30A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2	30	87.1	0.11	14.2	4.1		203918

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.25	91.3		0.41

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	FREE R-VALUE	2	15	48807	746	78.471	0.205	0.2043	0.2473	30.55

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]
0.081		0.038	-0.066		-0.029

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.13
r_dihedral_angle_4_deg	15.091
r_dihedral_angle_3_deg	13.9
r_dihedral_angle_1_deg	8.719
r_lrange_it	5.83
r_lrange_other	5.767
r_scangle_it	3.563
r_scangle_other	3.563
r_mcangle_it	3.323
r_mcangle_other	3.323
r_scbond_it	2.432
r_scbond_other	2.432
r_mcbond_it	2.326
r_mcbond_other	2.324
r_angle_refined_deg	1.529
r_angle_other_deg	1.257
r_xyhbond_nbd_refined	0.215
r_symmetry_nbd_other	0.194
r_nbd_refined	0.19
r_nbd_other	0.187
r_nbtor_refined	0.161
r_symmetry_xyhbond_nbd_refined	0.151
r_symmetry_nbd_refined	0.133
r_symmetry_xyhbond_nbd_other	0.108
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.062
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	6480
Nucleic Acid Atoms
Solvent Atoms	419
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing
RESOLVE	model building