4CVW | pdb_00004cvw

Structure of the barley limit dextrinase-limit dextrinase inhibitor complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Y4S	PDB ENTRIES 2Y4S AND 1B1U
experimental model	PDB	1B1U	PDB ENTRIES 2Y4S AND 1B1U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				PROTEIN STOCK: PURIFIED 1:1 ENZYME:INHIBITOR COMPLEX (A280NM = 12.1) IN 50 MM MES PH 6.6, 250 MM NACL, 0.5 MM CACL2. RESERVOIR: 24% POLYETHYLENE GLYCOL (PEG) 8000 AND 0.05 M KH2PO4. 0.5 MICROLITRE 0.1 M NAD WAS ADDED TO THE DROPLET TO A CONCENTRATION OF 0.01 M.

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 166.979	α = 90
b = 168.606	β = 90
c = 157.708	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	MARRESEARCH		2011-04-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2		ESRF	ID23-2

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	2.67	157.76	99.4	0.18	8	4.9		60740

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	2.67	2.85	99.7		0.68	2.2	4.4

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 ENTRIES 2Y4S AND 1B1U	2.67	157.76	57661	3078	96.3	0.257	0.255	0.21	0.293	0.24	RANDOM	24.8

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]
2.46			10.7		-13.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.791
r_dihedral_angle_3_deg	13.176
r_dihedral_angle_4_deg	12.929
r_dihedral_angle_1_deg	4.194
r_angle_refined_deg	0.847
r_scangle_it	0.444
r_mcangle_it	0.309
r_scbond_it	0.252
r_mcbond_it	0.167
r_chiral_restr	0.055
r_bond_refined_d	0.006
r_gen_planes_refined	0.003
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_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_mcbond_other
r_mcangle_other
r_scbond_other
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	15044
Nucleic Acid Atoms
Solvent Atoms	98
Heterogen Atoms	4

Software

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