3MBD | pdb_00003mbd

Crystal structure of fructose bisphosphate aldolase from Encephalitozoon cuniculi, bound to phosphate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QO5	PDB ENTRY 1QO5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	290	90% PACT SCREEN CONDITION F10, 10% ADDITIVE SCREEN G12: 90MM BIS-TRIS PROPANE PH 6.5, 18% PEG 3350, 18 MM NAKHPO4, 10 MM UREA, PROTEIN AT 24.7 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K

Crystal Properties
Matthews coefficient	Solvent content
3.41	63.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.96	α = 90
b = 137.61	β = 90
c = 62.23	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 210		2010-03-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.9774	ALS	5.0.1

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	36.8	99.8	0.056	21.83	6.2	35792	35720		-3

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	99.3		0.489	3.6	6.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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 1QO5	2	35.34	35792	33882	1749	99.58	0.16375	0.1624	0.17	0.19021	0.2	RANDOM	29.39

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]
-0.54			-0.98		1.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.385
r_dihedral_angle_4_deg	22.125
r_dihedral_angle_3_deg	13.748
r_dihedral_angle_1_deg	5.804
r_scangle_it	3.645
r_scbond_it	2.234
r_angle_refined_deg	1.395
r_mcangle_it	1.371
r_angle_other_deg	0.913
r_mcbond_it	0.763
r_mcbond_other	0.208
r_chiral_restr	0.09
r_bond_refined_d	0.015
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	2631
Nucleic Acid Atoms
Solvent Atoms	192
Heterogen Atoms	6

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling