4IYE | pdb_00004iye

Crystal structure of AdTx1 (rho-Da1a) from eastern green mamba (Dendroaspis angusticeps)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FF4	PDB ENTRY 1FF4 without loop 1 tip

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Lyophilization	8	273	Crystallization during lyophilization due to increased concentration and low temperature. Cryoconditions: 27% PEG8K, 15% MPEG550, 10% glycerol, 0.09 M Tris-HCl, pH 8.0, Lyophilization, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
1.82	32.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.37	α = 90
b = 37.37	β = 90
c = 66.05	γ = 120

Symmetry
Space Group	P 31 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 4	mirrors	2010-06-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.9334	ESRF	ID14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.95	32.36	93.9	0.171	0.16	11.43	8.44	4193	3937		-4	25.325

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2.07	69.1		1.088	0.947	1.12	2.89	660

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 1FF4 without loop 1 tip	1.951	32.36	-3	3937	3738	197	93.89	0.17545	0.17445	0.17033	0.17	0.25188	0.27	RANDOM	25.704

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]
1.63	1.63		1.63		-5.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.032
r_dihedral_angle_3_deg	14.462
r_sphericity_bonded	12.756
r_dihedral_angle_4_deg	9.449
r_dihedral_angle_1_deg	7.225
r_rigid_bond_restr	5.042
r_angle_refined_deg	1.648
r_angle_other_deg	1.233
r_chiral_restr	0.08
r_bond_refined_d	0.016

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.032
r_dihedral_angle_3_deg	14.462
r_sphericity_bonded	12.756
r_dihedral_angle_4_deg	9.449
r_dihedral_angle_1_deg	7.225
r_rigid_bond_restr	5.042
r_angle_refined_deg	1.648
r_angle_other_deg	1.233
r_chiral_restr	0.08
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	505
Nucleic Acid Atoms
Solvent Atoms	70
Heterogen Atoms	18

Software

Software
Software Name	Purpose
DNA	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.