9ISJ | pdb_00009isj

Crystal structure of Klebsiella pneumoniae ZapA

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	0.2 M Sodium acetate trihydrate, 0.1 M Sodium citrate pH5.5, and 10% PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.173	α = 90
b = 54.173	β = 90
c = 330.044	γ = 120

Symmetry
Space Group	P 61 2 2

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 EIGER X 16M		2023-07-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.0	SPring-8	BL41XU

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	1.8	46.45	99.84	0.999	20.03	9		28055

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	1.8	1.86			0.872

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.8	46.448	28052	1361	99.868	0.22	0.2186	0.2277	0.2393	0.2515	41.009

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]
0.008	0.004		0.008		-0.025

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.849
r_dihedral_angle_6_deg	15.807
r_dihedral_angle_2_deg	10.576
r_lrange_it	9.919
r_lrange_other	9.875
r_scangle_it	8.641
r_scangle_other	8.638
r_scbond_it	5.891
r_scbond_other	5.847
r_mcangle_other	5.083
r_mcangle_it	5.077
r_dihedral_angle_1_deg	4.387
r_mcbond_it	3.911
r_mcbond_other	3.904
r_angle_refined_deg	1.53
r_angle_other_deg	0.807
r_symmetry_nbd_refined	0.337
r_nbd_other	0.264
r_nbd_refined	0.224
r_symmetry_xyhbond_nbd_refined	0.204
r_symmetry_nbd_other	0.202
r_xyhbond_nbd_refined	0.18
r_nbtor_refined	0.177
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.077
r_bond_refined_d	0.01
r_gen_planes_other	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1712
Nucleic Acid Atoms
Solvent Atoms	132
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing