7WDV

Crystal structures of MeBglD2 in complex with various saccharides

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.1 M Tris-HCl buffer (pH 8.5), 1.2 M lithium sulfate, 0.01 M nickel chloride

Crystal Properties
Matthews coefficient	Solvent content
3.34	63.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 203.051	α = 90
b = 203.051	β = 90
c = 203.051	γ = 90

Symmetry
Space Group	I 4 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX300HE		2017-10-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9	SPring-8	BL44XU

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	1.81	50	100	0.086	77.5	33.6		64454

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	1.81	1.84			0.824

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	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5XGZ	1.812	30.002	64441	3209	99.95	0.159	0.1581	0.1848	RANDOM	18.54

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
r_dihedral_angle_6_deg	16.434
r_dihedral_angle_2_deg	15.195
r_dihedral_angle_3_deg	15.052
r_lrange_it	6.995
r_lrange_other	6.995
r_dihedral_angle_1_deg	6.483
r_scangle_it	5.475
r_scangle_other	5.474
r_scbond_it	3.53
r_scbond_other	3.529
r_mcangle_it	3.231
r_mcangle_other	3.231
r_mcbond_it	2.159
r_mcbond_other	2.159
r_angle_refined_deg	1.718
r_angle_other_deg	0.998
r_nbd_other	0.251
r_nbd_refined	0.228
r_symmetry_nbd_other	0.196
r_nbtor_refined	0.19
r_symmetry_nbd_refined	0.189
r_xyhbond_nbd_refined	0.171
r_symmetry_xyhbond_nbd_refined	0.165
r_symmetry_xyhbond_nbd_other	0.141
r_chiral_restr	0.105
r_symmetry_nbtor_other	0.08
r_bond_other_d	0.037
r_bond_refined_d	0.011
r_gen_planes_refined	0.011
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3598
Nucleic Acid Atoms
Solvent Atoms	394
Heterogen Atoms	55

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing