2WNC | pdb_00002wnc

Crystal structure of Aplysia ACHBP in complex with tropisetron

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				22% PEG4000, 0.1 M TRIS-HCL PH 7.5, 0.2 M LI2SO4

Crystal Properties
Matthews coefficient	Solvent content
3.2	61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 212.584	α = 90
b = 212.584	β = 90
c = 212.584	γ = 90

Symmetry
Space Group	I 2 3

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		2006-11-08	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	2.2	87	100	0.09	13.9	5.8		80567			35.7

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	2.32	100		0.5	3.4	5.9

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 2BYN	2.2	75.16	78146	2420	99.95	0.17837	0.17732	0.19	0.21171	0.22	RANDOM	37.5237

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	36.027
r_dihedral_angle_4_deg	22.446
r_dihedral_angle_3_deg	15.935
r_dihedral_angle_1_deg	6.201
r_scangle_it	2.778
r_scbond_it	1.951
r_angle_refined_deg	1.464
r_mcangle_it	1.175
r_mcbond_it	0.985
r_angle_other_deg	0.869
r_symmetry_vdw_other	0.25
r_nbd_other	0.205
r_nbd_refined	0.187
r_symmetry_vdw_refined	0.183
r_symmetry_hbond_refined	0.18
r_nbtor_refined	0.178
r_mcbond_other	0.161
r_xyhbond_nbd_refined	0.153
r_nbtor_other	0.087
r_chiral_restr	0.08
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_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	8491
Nucleic Acid Atoms
Solvent Atoms	611
Heterogen Atoms	105

Software

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