6B9J | pdb_00006b9j

Structure of vaccinia virus D8 protein bound to human Fab vv138

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4E9O	4E9O, 1RZ7
experimental model	PDB	1RZ7	4E9O, 1RZ7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	295	20% PEG 3350, 200mM sodium malonate

Crystal Properties
Matthews coefficient	Solvent content
3.67	66.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 234.282	α = 90
b = 253.842	β = 90
c = 73.76	γ = 90

Symmetry
Space Group	C 2 2 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		2014-03-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	1.15	SSRL	BL7-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	2.905	172.163	99.4	0.163	0.179	0.071	8.3	6.2	48731	48731

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	3.06	99.8		1.433	1.433	1.559	0.607	0.5	6.4

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4E9O, 1RZ7	2.9	117.14	46251	2466	99.22	0.2426	0.2412	0.2689	0.255	RANDOM	87.27

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]
-0.01			0.02		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.816
r_dihedral_angle_3_deg	14.876
r_dihedral_angle_4_deg	12.271
r_dihedral_angle_1_deg	6.237
r_angle_refined_deg	1.197
r_angle_other_deg	0.924
r_chiral_restr	0.064
r_bond_refined_d	0.007
r_bond_other_d	0.006
r_gen_planes_refined	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9917
Nucleic Acid Atoms
Solvent Atoms	48
Heterogen Atoms	19

Software

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