4AIO | pdb_00004aio

Crystal structure of the starch debranching enzyme barley limit dextrinase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Y4S	PDB ENTRY 2Y4S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				PROTEIN STOCK: 10 MG/ML PROTEIN 50 MM MES PH 6.6, 250 MM NACL, 0.5 MM CACL2 AND 0.67 MM MALTOTRIOSE. RESERVOIR: 30% POLYETHYLENE GLYCOL (PEG) 3350, 5% GLYCEROL, AND 0.3 M NAI. CYSTEIN WAS ADDED TO THE DROPS TO A FINAL CONCENTRATION OF 5-7 MM

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 176.058	α = 90
b = 82.072	β = 96.2
c = 59.378	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	ADSC QUANTUM 315r		2010-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1		ESRF	ID23-1

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	1.9	35.54	91.3	0.04	7.8	2.6		60352

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	1.9	2	94.5		0.04	2.1	2.5

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 (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 2Y4S	1.9	33.694	57222	3081	91.02	0.18871	0.18678	0.19	0.22476	0.22	RANDOM	20.828

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]
		0.09	-0.02		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.7
r_dihedral_angle_4_deg	19.014
r_dihedral_angle_3_deg	12.755
r_dihedral_angle_1_deg	5.55
r_angle_refined_deg	1.165
r_symmetry_vdw_refined	0.195
r_symmetry_hbond_refined	0.155
r_xyhbond_nbd_refined	0.112
r_chiral_restr	0.082
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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	6755
Nucleic Acid Atoms
Solvent Atoms	294
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing