7X4D | pdb_00007x4d

Crystal structure of chlorotoxin mutant - Y29K

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7X41

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	1 M monosodium phosphate and 0.75 M sodium citrate

Crystal Properties
Matthews coefficient	Solvent content
1.57	21.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 22.393	α = 90
b = 25.941	β = 90
c = 47.312	γ = 90

Symmetry
Space Group	P 21 21 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	CCD	ADSC QUANTUM 315r		2016-05-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13B1	1.00000	NSRRC	BL13B1

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	1.55	30	98.31	0.058	22.9	3.5		4274

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	1.55	1.61			0.139

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	THROUGHOUT	7X41	1.55	23.656	4249	204	98.311	0.14	0.1375	0.15	0.187	0.19	9.313

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]
-0.482			0.203		0.279

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.641
r_dihedral_angle_4_deg	18.027
r_dihedral_angle_3_deg	13.239
r_dihedral_angle_1_deg	7.89
r_rigid_bond_restr	2.652
r_scangle_it	2.478
r_scangle_other	2.446
r_scbond_it	2.298
r_lrange_it	2.284
r_lrange_other	2.137
r_scbond_other	2.121
r_angle_refined_deg	1.476
r_angle_other_deg	1.451
r_mcangle_it	1.183
r_mcangle_other	1.181
r_mcbond_it	0.963
r_mcbond_other	0.88
r_nbd_refined	0.216
r_symmetry_nbd_other	0.195
r_symmetry_nbd_refined	0.192
r_nbtor_refined	0.154
r_nbd_other	0.147
r_symmetry_xyhbond_nbd_refined	0.097
r_xyhbond_nbd_refined	0.095
r_chiral_restr	0.085
r_symmetry_nbtor_other	0.085
r_gen_planes_refined	0.014
r_bond_refined_d	0.01
r_gen_planes_other	0.005
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	271
Nucleic Acid Atoms
Solvent Atoms	34
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
HKL-3000	phasing