2AV6 | pdb_00002av6

X-Ray studies on maltodextrin phosphorylase complexes: recognition of substrates and cathalitic mechanism of phosphorylase family

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1L5V	PDB ENTRY 1L5V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	PEG4000, Lithium chloride, TRIS (hydroxymethil) aminomethane, maltopentaose, alluminium nitrate, sodium fluoride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.957	α = 90
b = 105.614	β = 90
c = 218.629	γ = 90

Symmetry
Space Group	P 21 21 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	IMAGE PLATE	MARRESEARCH	MIRRORS		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	1.2	ELETTRA	5.2R

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	2.01	111.8		0.149	6.7	2.1	102161	100613			21.8

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	2.01	2.11			0.447	2	1.9	10682

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 1L5V	2.01	15	95530	5058	86.29	0.1927	0.18998	0.2	0.24387	0.19	RANDOM	24.683

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]
-0.97			-1.15		2.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.59
r_scangle_it	3.898
r_angle_other_deg	3.762
r_scbond_it	2.407
r_angle_refined_deg	1.667
r_mcangle_it	1.501
r_mcbond_it	0.85
r_symmetry_vdw_other	0.327
r_nbd_other	0.281
r_nbd_refined	0.22
r_symmetry_vdw_refined	0.188
r_symmetry_hbond_refined	0.166
r_xyhbond_nbd_refined	0.164
r_nbtor_other	0.109
r_chiral_restr	0.107
r_bond_refined_d	0.02
r_gen_planes_other	0.011
r_gen_planes_refined	0.008
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12778
Nucleic Acid Atoms
Solvent Atoms	1145
Heterogen Atoms	150

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling