2H39 | pdb_00002h39

Crystal Structure of an ADP-Glucose Phosphorylase from Arabidopsis thaliana with bound ADP-Glucose

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Z84	PDB Entry: 1Z84

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	10 MG/ML PROTEIN, 20% PEG 2000, 0.2M SODIUM CHLORIDE, 0.10M MES-ACETATE, vapor diffusion, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.318	α = 90
b = 95.454	β = 90
c = 110.504	γ = 90

Symmetry
Space Group	P 21 21 21

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	BRUKER PROTEUM-R	MONTEL OPTICS	2005-09-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.5418

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	2.23	47.73	100	0.1912	11.28	11.78		32389

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)
	2.23	2.25	99.9		0.6756	2.92	7.34	840

Refinement

Statistics
Diffraction ID	Structure Solution 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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB Entry: 1Z84	2.23	47.727	32302	1639	99.91	0.179	0.1761	0.18	0.2434	0.24	18.776

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]
0.031			-0.031		0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.761
r_dihedral_angle_4_deg	25.756
r_dihedral_angle_3_deg	14.842
r_dihedral_angle_1_deg	6.73
r_scbond_it	3.722
r_scangle_it	2.784
r_mcangle_it	2.73
r_angle_refined_deg	1.664
r_mcbond_it	1.516
r_nbtor_refined	0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.761
r_dihedral_angle_4_deg	25.756
r_dihedral_angle_3_deg	14.842
r_dihedral_angle_1_deg	6.73
r_scbond_it	3.722
r_scangle_it	2.784
r_mcangle_it	2.73
r_angle_refined_deg	1.664
r_mcbond_it	1.516
r_nbtor_refined	0.31
r_symmetry_vdw_refined	0.287
r_nbd_refined	0.201
r_symmetry_hbond_refined	0.188
r_metal_ion_refined	0.178
r_xyhbond_nbd_refined	0.162
r_chiral_restr	0.111
r_bond_refined_d	0.017
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4904
Nucleic Acid Atoms
Solvent Atoms	371
Heterogen Atoms	82

Software

Software
Software Name	Purpose
SAINT	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.