4LDB | pdb_00004ldb

Crystal Structure of Ebola Virus VP40 Dimer

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	293	0.05 M magnesium chloride, 0.1 M HEPES, 38% PEG400, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 160.005	α = 90
b = 160.005	β = 90
c = 89.745	γ = 120

Symmetry
Space Group	P 62

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	85	PIXEL	DECTRIS PILATUS 6M		2010-05-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.97945	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.27	50	83.7			60525	50678		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.27

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	3.1	50	24108	22689	1218	99.97	0.24693	0.245	0.2447	0.282	0.2761	RANDOM	67.165

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]
3.68	1.84		3.68		-5.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.071
r_dihedral_angle_4_deg	16.327
r_dihedral_angle_3_deg	12.101
r_scangle_it	4.571
r_dihedral_angle_1_deg	4.172
r_scbond_it	2.496
r_mcangle_it	2.327
r_mcbond_it	1.233
r_angle_refined_deg	0.558
r_chiral_restr	0.031
r_bond_refined_d	0.009
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7574
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

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