7QHI | pdb_00007qhi

Crystal structure of cytotoxin 13 from Naja naja, hexagonal 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	COUNTER-DIFFUSION		273	Sodium chloride, K/NaPhosphate,MES pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
	74.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.331	α = 90
b = 109.331	β = 90
c = 135.77	γ = 120

Symmetry
Space Group	P 64 2 2

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 EIGER X 16M		2016-06-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.0000	SPring-8	BL41XU

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	2.3	50	98.39	0.104	13.4	8.2		21512

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	2.3	2.36			0.54	2.3

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	2.302	14.9	21512	1034	98.386	0.2	0.1987	0.2	0.2283	0.21	39.558

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]
-0.008	-0.004		-0.008		0.025

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_4_deg	24.632
r_dihedral_angle_2_deg	22.604
r_dihedral_angle_3_deg	19.972
r_dihedral_angle_1_deg	10.474
r_lrange_it	7.999
r_lrange_other	7.648
r_scangle_other	4.864
r_scangle_it	4.863
r_mcangle_it	3.603
r_mcangle_other	3.602
r_scbond_other	3.052
r_scbond_it	3.048
r_mcbond_it	2.134
r_mcbond_other	2.134
r_angle_refined_deg	2.094
r_angle_other_deg	1.327
r_xyhbond_nbd_refined	0.335
r_symmetry_nbd_refined	0.325
r_nbd_refined	0.234
r_nbd_other	0.234
r_symmetry_nbd_other	0.221
r_symmetry_xyhbond_nbd_other	0.2
r_symmetry_xyhbond_nbd_refined	0.186
r_nbtor_refined	0.17
r_chiral_restr	0.1
r_symmetry_nbtor_other	0.097
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1392
Nucleic Acid Atoms
Solvent Atoms	217
Heterogen Atoms

Software

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