9SD7 | pdb_00009sd7

Crystal structure of C-terminally truncated human PGGHG in complex with glucose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9SD4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.2	289	Precipitant ratio 1:1 Co-crystallized 5% (0.27 mM) Glucose. Condition: 22.4% PEG 3350, 0.1 M Bis-Tris pH 6.2, 0.2 M MgCl2

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.021	α = 90
b = 77.382	β = 99.68
c = 78.814	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 PILATUS 6M		2021-10-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97918	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.39	77.692	92.84	0.036	0.9979	11.003	6.32		105192			17.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.393	1.49	50.41		0.413	0.5655	1.244	4.46

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.39	77.69	99863	5329	82.43	0.15345	0.15204	0.1517	0.17997	0.1797	RANDOM	17.666

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]
-0.07		0.08	-0.06		0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.086
r_dihedral_angle_2_deg	9.581
r_dihedral_angle_1_deg	6.708
r_long_range_B_refined	6.193
r_long_range_B_other	5.988
r_scangle_other	4.716
r_scbond_it	3.055
r_scbond_other	3.055
r_mcangle_it	2.691
r_mcangle_other	2.69
r_angle_refined_deg	1.828
r_mcbond_it	1.801
r_mcbond_other	1.8
r_angle_other_deg	0.66
r_chiral_restr	0.102
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_bond_other_d	0.003
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5322
Nucleic Acid Atoms
Solvent Atoms	694
Heterogen Atoms	44

Software

Software
Software Name	Purpose
autoPROC	data processing
MOLREP	phasing
REFMAC	refinement
Coot	model building
PDB_EXTRACT	data extraction