1UMR | pdb_00001umr

Crystal structure of the platelet activator convulxin, a disulfide linked a4b4 cyclic tetramer from the venom of Crotalus durissus terrificus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1C3A	PDB ENTRY 1C3A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.6		pH 4.60

Crystal Properties
Matthews coefficient	Solvent content
4.8	73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.906	α = 90
b = 131.906	β = 90
c = 112.849	γ = 90

Symmetry
Space Group	I 4

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	ROTATING ANODE	RIGAKU RU300

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	2.4	30	97.6	0.061	12.1	2.4		36900		2

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	2.4	2.6	98.8		0.404	1.9

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 1C3A	2.4	30	34998	1845	97.6	0.19	0.187	0.2	0.264	0.27	RANDOM	47.25

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]
1.16			1.16		-2.33

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	8.456
r_dihedral_angle_1_deg	8.429
r_scbond_it	7.103
r_mcangle_it	6.529
r_mcbond_it	4.971
r_angle_refined_deg	2.693
r_symmetry_vdw_refined	0.447
r_nbd_refined	0.256
r_xyhbond_nbd_refined	0.212
r_chiral_restr	0.207
r_symmetry_hbond_refined	0.194
r_bond_refined_d	0.033
r_gen_planes_refined	0.015
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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	4318
Nucleic Acid Atoms
Solvent Atoms	197
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing