Experiment: 9VEP

Crystal structure of Klebsiella pneumoniae SuhB

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6IB7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	PEG 3350, Sodium formate

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.2	α = 90
b = 88.281	β = 97.73
c = 66.097	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	IMAGE PLATE	MAR scanner 345 mm plate		2025-05-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	RRCAT INDUS-2 BEAMLINE PX-BL21	0.97893	RRCAT INDUS-2	PX-BL21

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	1.7	45.78	99.2	0.999	21.6	5.9		57326			16.88

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	1.7	1.79	98.6		0.963	5.7	5.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6IB7	1.7	40.64	1.34	57302	2852	99.22	0.1481	0.1464	0.1446	0.18	0.1765	24.25

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	6.0841
f_angle_d	0.913
f_chiral_restr	0.0569
f_plane_restr	0.0096
f_bond_d	0.0061

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4069
Nucleic Acid Atoms
Solvent Atoms	445
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing