6R5T | pdb_00006r5t

The crystal structure of Glycoside Hydrolase BglX inactive mutant D286N from P. aeruginosa in complex with lactose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5TF0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	100 mM Bis Tris, pH 5.5, 17% PEG 10000 and 100 mM ammonium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.978	α = 65.55
b = 73.588	β = 73.42
c = 81.124	γ = 69.68

Symmetry
Space Group	P 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 PILATUS 6M		2017-09-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.979257	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.6	45.17	96.1	0.05	10.8	3.3		175334

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.63			0.51

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	5tf0	1.6	45.17	166499	8830	96.12	0.14082	0.13935	0.1528	0.1684	0.1776	RANDOM	20.863

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]
0.31	0.13	-1.1	-0.44	0.98	0.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.61
r_dihedral_angle_4_deg	19.985
r_dihedral_angle_3_deg	13.109
r_dihedral_angle_1_deg	6.779
r_long_range_B_refined	6.524
r_long_range_B_other	6.523
r_scangle_other	4.888
r_scbond_it	3.207
r_scbond_other	3.206
r_mcangle_it	2.471
r_mcangle_other	2.471
r_angle_refined_deg	1.81
r_mcbond_it	1.787
r_mcbond_other	1.786
r_angle_other_deg	1.594
r_chiral_restr	0.093
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	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	11274
Nucleic Acid Atoms
Solvent Atoms	1392
Heterogen Atoms	86

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing