7E9W

The Crystal Structure of D-psicose-3-epimerase from Biortus.

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.02M MgCl2, 0.1M HEPES pH7.5, 22% Polyacrylic acid sodium salt 5,100

Crystal Properties
Matthews coefficient	Solvent content
3.11	60.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.134	α = 90
b = 116.083	β = 105.083
c = 91.817	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	PIXEL	DECTRIS PILATUS3 6M		2021-02-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	1.5215	CLSI	08ID-1

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	2.1	48.607	98	0.998	10.2	3.4		91449

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	2.1	2.14			0.829

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3vni	2.1	48.607	91439	4559	97.957	0.175	0.1737	0.2058	34.161

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]
0.358		1.476	-0.369		-0.685

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.172
r_dihedral_angle_4_deg	15.004
r_dihedral_angle_3_deg	13.96
r_dihedral_angle_1_deg	6.544
r_lrange_it	4.53
r_lrange_other	4.434
r_scangle_it	2.912
r_scangle_other	2.912
r_mcangle_it	2.327
r_mcangle_other	2.326
r_scbond_it	1.873
r_scbond_other	1.872
r_mcbond_it	1.441
r_mcbond_other	1.44
r_angle_refined_deg	1.22
r_angle_other_deg	1.193
r_nbd_refined	0.187
r_nbd_other	0.176
r_symmetry_nbd_other	0.171
r_nbtor_refined	0.16
r_xyhbond_nbd_refined	0.146
r_symmetry_nbd_refined	0.118
r_symmetry_xyhbond_nbd_refined	0.084
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.053
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9212
Nucleic Acid Atoms
Solvent Atoms	574
Heterogen Atoms	76

Software

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