3MBF | pdb_00003mbf

Crystal structure of fructose bisphosphate aldolase from Encephalitozoon cuniculi, bound to fructose 1,6-bisphosphate

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3MDB	PDB entry 3MDB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	290	BASED ON PACT SCREEN CONDITION F10 WITHOUT NAKHPO4: 100MM BIS-TRIS PROPANE PH 6.5, 20% PEG 3350, 20 MM FRUCTOSE 1,6-BISPHOSPHATE, PROTEIN AT 24.7 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K

Crystal Properties
Matthews coefficient	Solvent content
3.32	62.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.46	α = 90
b = 135.82	β = 90
c = 61.54	γ = 90

Symmetry
Space Group	C 2 2 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	ADSC QUANTUM 315		2010-03-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	0.977400	SSRL	BL7-1

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	2.37	28.03	99.7	0.081	15.35	4.4	21111	21046		-3	37.35

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	2.37	2.43	99.6		0.479	3.2	4.4	1557

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	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 3MDB	2.37	28.03	20970	1022		0.167	0.165	0.16	0.208	0.2	To match 3MBD (random)	24.84

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]
-1.28			-0.44		1.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.606
r_dihedral_angle_4_deg	19.307
r_dihedral_angle_3_deg	15.33
r_dihedral_angle_1_deg	6.078
r_scangle_it	3.871
r_scbond_it	2.35
r_angle_refined_deg	1.499
r_mcangle_it	1.36
r_angle_other_deg	0.9
r_mcbond_it	0.711
r_mcbond_other	0.169
r_chiral_restr	0.083
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2617
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms	19

Software

Software
Software Name	Purpose
Blu-Ice	data collection
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing