5DU1 | pdb_00005du1

Crystal structure of Dendroaspis polylepis mambalgin-1 wild-type in P21 space group.

X-RAY DIFFRACTION

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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	6	293	protein: 5 mg/mL in 0.550 M Na Acetate pH 5.5 precipitant: 18% PEG4K, 3% MPD, 3% 1,4-dioxane, .188 M Imidazole Malate, pH 6 cryoprotectant:: CrySol-SM5, 30% PEG 600, 0.1 M mixed (Na acetate, ADA, Bicine), pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
1.74	29.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.03	α = 90
b = 50.24	β = 93.38
c = 46.88	γ = 90

Symmetry
Space Group	P 1 21 1

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 2M	Compound Refractive Lens Fully automatic data collection	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	1.8	46.796	93.8	0.063	0.052	13.77	2.7	15969	15969		-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	1.8	1.91	84.7		0.257	4.35	2.77

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	5DO6	1.8	38.96	15332	807	95.3	0.17662	0.17406	0.19	0.22433	0.24	RANDOM	27.705

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]
3.11		0.22	-1.22		-1.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.855
r_dihedral_angle_4_deg	21.029
r_dihedral_angle_3_deg	17.159
r_long_range_B_refined	9.462
r_long_range_B_other	9.446
r_dihedral_angle_1_deg	7.997
r_scangle_other	5.76
r_mcangle_other	4.125
r_mcangle_it	4.123
r_scbond_it	3.723
r_scbond_other	3.715
r_mcbond_it	2.696
r_mcbond_other	2.676
r_angle_other_deg	2.375
r_angle_refined_deg	2.065
r_chiral_restr	0.103
r_bond_refined_d	0.019
r_bond_other_d	0.013
r_gen_planes_refined	0.013
r_gen_planes_other	0.011
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1804
Nucleic Acid Atoms
Solvent Atoms	196
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
Coot	model building