7QFC | pdb_00007qfc

Crystal structure of cytotoxin 13 from Naja naja, orthorhombic form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RL5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.5	293	NaCl, sodium dihydrogen phosphate, 0.1M MES pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
3.51	64.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.759	α = 90
b = 97.175	β = 90
c = 131.917	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	PIXEL	DECTRIS PILATUS 12M		2016-06-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.9763	PETRA III, EMBL c/o DESY	P14 (MX2)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.6	50	99.17	0.2	1.8	6.3		18995

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.63	99.6		0.89

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1RL5	2.6	14.89	17772	874	99.196	0.207	0.2049	0.21	0.2547	0.21	93.644

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]
0.722			-0.371		-0.351

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.225
r_dihedral_angle_3_deg	24.148
r_dihedral_angle_4_deg	23.606
r_lrange_it	11.11
r_lrange_other	11.109
r_dihedral_angle_1_deg	10.277
r_scangle_it	7.627
r_scangle_other	7.612
r_mcangle_it	6.952
r_mcangle_other	6.951
r_scbond_it	4.822
r_scbond_other	4.789
r_mcbond_it	4.355
r_mcbond_other	4.353
r_angle_refined_deg	2.191
r_angle_other_deg	1.278
r_symmetry_nbd_refined	0.254
r_nbd_refined	0.226
r_symmetry_nbd_other	0.223
r_nbd_other	0.221
r_xyhbond_nbd_refined	0.198
r_nbtor_refined	0.185
r_symmetry_xyhbond_nbd_other	0.134
r_symmetry_nbtor_other	0.098
r_chiral_restr	0.083
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_gen_planes_other	0.005
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2784
Nucleic Acid Atoms
Solvent Atoms	17
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing