2ZJ4 | pdb_00002zj4

Isomerase domain of human glucose:fructose-6-phosphate amidotransferase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ZJ3	PDB ENTRY 2ZJ3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	277	12% Isoporpanol, 0.04M Tris, 0.08M Ammonium acetate, 12% glycerol 10-fold excess of 2-deoxy-2-aminoglucitol-6-phosphate, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.927	α = 90
b = 78.927	β = 90
c = 277.323	γ = 90

Symmetry
Space Group	I 41 2 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	IMAGE PLATE	RIGAKU RAXIS V		2003-08-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL32B2		SPring-8	BL32B2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	39.53	98.4				22501

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 (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	PDB ENTRY 2ZJ3	2.2	38	21357	1144	98.39	0.16	0.158	0.17	0.208	0.17	RANDOM	20.568

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]
0.01			0.01		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.79
r_dihedral_angle_4_deg	20.724
r_dihedral_angle_3_deg	15.697
r_dihedral_angle_1_deg	6.404
r_scangle_it	4.334
r_scbond_it	3.106
r_angle_refined_deg	1.778
r_mcangle_it	1.612
r_angle_other_deg	1.454
r_mcbond_it	1.437
r_symmetry_vdw_other	0.289
r_symmetry_hbond_refined	0.24
r_mcbond_other	0.238
r_nbd_refined	0.23
r_nbd_other	0.196
r_symmetry_vdw_refined	0.187
r_xyhbond_nbd_refined	0.185
r_nbtor_refined	0.171
r_chiral_restr	0.121
r_nbtor_other	0.088
r_bond_refined_d	0.021
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2863
Nucleic Acid Atoms
Solvent Atoms	267
Heterogen Atoms	16

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing