5LXB | pdb_00005lxb

Crystal structure of a mutant binding protein (5HTBP-AChBP) in complex with palonosetron

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	200 mM sodium 265 citrate, 100 mM bis tris propane pH 8.5, and 20% (w/v) PEG3350.

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.215	α = 90
b = 137.051	β = 93.78
c = 131.249	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS PILATUS 300K		2004-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.873	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.34	130.96	99.2	8.9	4.5		106052

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.34	2.47	94.5		0.845	0.598	1.6	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	2yme	2.34	130.96	100742	5294	98.82	0.2192	0.2179	0.23	0.245	0.25	RANDOM	55.902

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]
-0.76		2.23	0.45		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.352
r_dihedral_angle_4_deg	19.999
r_dihedral_angle_3_deg	14.042
r_dihedral_angle_1_deg	6.754
r_mcangle_it	4.174
r_mcbond_it	2.921
r_mcbond_other	2.921
r_angle_refined_deg	1.819
r_angle_other_deg	1.005
r_chiral_restr	0.102
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16400
Nucleic Acid Atoms
Solvent Atoms	280
Heterogen Atoms	266

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SCALA	data scaling
MOLREP	phasing