3A4A | pdb_00003a4a

Crystal structure of isomaltase from Saccharomyces cerevisiae

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3A47	PDB ENTRY 3A47

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.3	288	19% PEG 3350, 0.05M HEPES, 0.2M lithium acetate, 0.2M maltose, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 288K

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.428	α = 90
b = 115.404	β = 91.19
c = 61.606	γ = 90

Symmetry
Space Group	C 1 2 1

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 DIP-6040		2007-04-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.90000	SPring-8	BL44XU

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	1.6	25	99.7	0.042	25.8	0.042	87616	87353	2	2

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)
	1.6	1.66	97.4		0.05	13.8	4.1	8761

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 (All)	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 3A47	1.6	23	83213	82972	4375	99.71	0.15958	0.15946	0.15867	0.1575	0.17426	0.1726	RANDOM	11.85

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.435
r_dihedral_angle_4_deg	16.902
r_dihedral_angle_3_deg	11.482
r_dihedral_angle_1_deg	5.929
r_scangle_it	2.534
r_scbond_it	1.599
r_angle_refined_deg	1.173
r_mcangle_it	1.021
r_mcbond_it	0.604
r_nbtor_refined	0.313
r_nbd_refined	0.197
r_symmetry_vdw_refined	0.17
r_symmetry_hbond_refined	0.168
r_metal_ion_refined	0.121
r_xyhbond_nbd_refined	0.088
r_chiral_restr	0.087
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4835
Nucleic Acid Atoms
Solvent Atoms	582
Heterogen Atoms	13

Software

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