5DZ5 | pdb_00005dz5

Crystal structure of Dendroaspis polylepis mambalgin-1 wild-type in P41212 space group

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5DO6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	Protein: 5 mg/mL in 0.050 M Na Acetate, pH 5.5 Precipitant: 30% PEG600, 0.2 M Imidazole Malate, pH 7.0. Cryoprotectant: 40% CryoSol SM5, 30% PEG 600, 0.1 M mixed (Na acetate, ADA, Bicine) pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
1.68	26.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.8	α = 90
b = 46.8	β = 90
c = 80.56	γ = 90

Symmetry
Space Group	P 41 21 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 PILATUS 6M	automatic data collection on ESRF Massif1 ID30A-1	2015-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.965	ESRF	MASSIF-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	46.8	99.9	0.183	0.171	9.66	7.5	6985	6981		-3

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	1.95	2	100		1.67	1.19	7.94

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	FREE R-VALUE	5DO6	1.95	40.467	1.35	6979	349	99.91	0.1949	0.192	0.2	0.2459	0.24	Random selection

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.1
f_angle_d	1.991
f_chiral_restr	0.112
f_bond_d	0.025
f_plane_restr	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	902
Nucleic Acid Atoms
Solvent Atoms	80
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
PHASER	phasing
XSCALE	data scaling
MxCuBE	data collection
Coot	model building
XDS	data reduction

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.