6UBC | pdb_00006ubc

Crystal structure of a GH128 (subgroup VII) oligosaccharide-binding protein from Cryptococcus neoformans (CnGH128_VII)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	291	Sodium acetate 0.1 M ammonium sulfate 2.0 M

Crystal Properties
Matthews coefficient	Solvent content
1.48	16.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.41	α = 90
b = 118.41	β = 90
c = 118.41	γ = 90

Symmetry
Space Group	I 2 3

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		2018-05-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.979460	SSRL	BL12-2

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	1.65	48.39	99.8	0.999	16.65	40.1		33192

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	1.65	1.75			0.589

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 (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.65	48.39	31648	1587	99.92	0.1721	0.1703	0.2075	0.1955	RANDOM	27.362

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	34.6
r_dihedral_angle_3_deg	13.334
r_dihedral_angle_4_deg	13.197
r_dihedral_angle_1_deg	6.549
r_mcangle_it	2.608
r_angle_other_deg	2.503
r_mcbond_it	1.878
r_mcbond_other	1.874
r_angle_refined_deg	1.826
r_chiral_restr	0.092
r_bond_other_d	0.038
r_gen_planes_other	0.023
r_bond_refined_d	0.015
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1948
Nucleic Acid Atoms
Solvent Atoms	298
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing