8V31 | pdb_00008v31

Structure of Alistipes sp. 3-Keto-2-hydroxy-glucal-hydratase AL2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	298	0.2 M Magnesium Chloride, 25% PEG 3350, 0.1 M Bis-Tris methane pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
3.36	63.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.088	α = 90
b = 95.088	β = 90
c = 159.542	γ = 120

Symmetry
Space Group	P 31 2 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 S 6M		2023-07-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08B1-1	1.18085	CLSI	08B1-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.65	47.54	99.9	0.142	0.15	0.047	0.999	22.9	18.9		24911

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.65	2.78			2.057	2.176	0.704	0.868		18.5

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	2.65	47.54	24670	1229	99.12	0.199	0.1966	0.21	0.2441	0.25	61.222

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]
0.78	0.39		0.78		-2.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	20.301
r_dihedral_angle_2_deg	20.262
r_dihedral_angle_6_deg	15.754
r_lrange_other	13.943
r_lrange_it	13.937
r_scangle_it	13.22
r_scangle_other	13.217
r_scbond_it	10.531
r_scbond_other	10.497
r_mcangle_it	10.367
r_mcangle_other	10.365
r_dihedral_angle_1_deg	8.891
r_mcbond_it	8.552
r_mcbond_other	8.503
r_angle_refined_deg	2.654
r_angle_other_deg	0.878
r_symmetry_nbd_refined	0.275
r_symmetry_nbd_other	0.224
r_nbd_refined	0.212
r_nbtor_refined	0.198
r_nbd_other	0.173
r_xyhbond_nbd_refined	0.154
r_chiral_restr	0.116
r_symmetry_nbtor_other	0.1
r_bond_refined_d	0.015
r_gen_planes_refined	0.013
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3938
Nucleic Acid Atoms
Solvent Atoms	40
Heterogen Atoms	2

Software

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