7WDO | pdb_00007wdo

Crystal structures of MeBglD2 in complex with various saccharides

X-RAY DIFFRACTION

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Starting Model(s)

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

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
3.38	63.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 203.84	α = 90
b = 203.84	β = 90
c = 203.84	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		2016-05-19	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	2.2	50	100	0.101	57.5	20.7		36279

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	2.2	2.24			0.468

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5XGZ	2.21	30.002	36245	1868	99.893	0.164	0.1623	0.17	0.1959	0.2	RANDOM	30.421

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_2_deg	23.159
r_dihedral_angle_3_deg	16.577
r_dihedral_angle_6_deg	16.399
r_lrange_other	7.005
r_lrange_it	7.004
r_dihedral_angle_1_deg	6.964
r_scangle_it	5.555
r_scangle_other	5.554
r_mcangle_other	4.276
r_mcangle_it	4.274
r_scbond_it	3.909
r_scbond_other	3.908
r_mcbond_it	2.95
r_mcbond_other	2.936
r_angle_refined_deg	1.688
r_angle_other_deg	1.12
r_nbd_other	0.384
r_symmetry_nbd_refined	0.342
r_nbd_refined	0.22
r_symmetry_xyhbond_nbd_refined	0.204
r_symmetry_nbd_other	0.199
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.151
r_chiral_restr	0.079
r_symmetry_nbtor_other	0.079
r_bond_other_d	0.041
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3602
Nucleic Acid Atoms
Solvent Atoms	265
Heterogen Atoms	45

Software

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