1GYN

Class II fructose 1,6-bisphosphate aldolase with Cadmium (not Zinc) in the active site

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZEN	PDB ENTRY 1ZEN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.6		pH 7.60

Crystal Properties
Matthews coefficient	Solvent content
3.22	61.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.331	α = 90
b = 77.331	β = 90
c = 290.851	γ = 120

Symmetry
Space Group	P 61 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	277	IMAGE PLATE	FUJI			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14		ESRF	BM14

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	38.3	86.9	0.057	12.8	2.5		31355

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	2.05	51		0.294	1.3	1.5

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1ZEN	2	38.35	29766	1580	87.2	0.169	0.168	0.193	RANDOM	25.16

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]
-0.16	-0.08		-0.16		0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.971
r_scangle_it	6.838
r_dihedral_angle_1_deg	5.443
r_scbond_it	4.331
r_mcangle_it	2.771
r_angle_refined_deg	2.56
r_mcbond_it	1.606
r_angle_other_deg	1.243
r_nbtor_other	0.346
r_metal_ion_refined	0.325
r_symmetry_vdw_refined	0.276
r_nbd_refined	0.253
r_nbd_other	0.215
r_symmetry_vdw_other	0.189
r_chiral_restr	0.182
r_xyhbond_nbd_refined	0.153
r_symmetry_hbond_refined	0.114
r_bond_refined_d	0.02
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2538
Nucleic Acid Atoms
Solvent Atoms	161
Heterogen Atoms	5

Software

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