9US5 | pdb_00009us5

Domain N deletion mutant of Klebsiella pneumoniae maltohexaose-producing alpha-amylase in complex with maltohexaose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9US3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	3.0~3.2 M NaCl 1 mM CaCl2 0.1 M Tris-HCl pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
3.64	66.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 163.084	α = 90
b = 163.084	β = 90
c = 139.376	γ = 90

Symmetry
Space Group	I 4 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	95	PIXEL	DECTRIS PILATUS 2M		2021-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0000	Photon Factory	AR-NW12A

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	2.66	100	100	0.121	29.3	26.3		27247

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	2.66	2.8			1.671	2.5

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	9US3	2.66	43.06	27242	1362	99.919	0.184	0.1818	0.1849	0.2259	0.2266	70.415

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]
0.024			0.024		-0.047

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.395
r_dihedral_angle_3_deg	15.698
r_dihedral_angle_4_deg	11.617
r_lrange_it	7.261
r_lrange_other	7.25
r_dihedral_angle_1_deg	6.981
r_scangle_other	5.049
r_scangle_it	5.046
r_mcangle_it	4.633
r_mcangle_other	4.633
r_scbond_it	3.026
r_scbond_other	3.014
r_mcbond_it	2.919
r_mcbond_other	2.918
r_angle_refined_deg	1.234
r_angle_other_deg	1.14
r_nbd_refined	0.182
r_symmetry_nbd_other	0.174
r_nbd_other	0.173
r_xyhbond_nbd_refined	0.162
r_nbtor_refined	0.16
r_metal_ion_refined	0.144
r_symmetry_xyhbond_nbd_refined	0.106
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.044
r_symmetry_nbd_refined	0.042
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4430
Nucleic Acid Atoms
Solvent Atoms	84
Heterogen Atoms	47

Software

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