6OTC | pdb_00006otc

Synthetic Fab bound to Marburg virus VP35 interferon inhibitory domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4GHL	PDB entries 4GHL & 1TZI
experimental model	PDB	1TZI	PDB entries 4GHL & 1TZI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293.15	10 mM Bis-Tris, pH 6.5, 20% PEG5000 MME

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.827	α = 90
b = 97.422	β = 90
c = 110.325	γ = 90

Symmetry
Space Group	P 21 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	CCD	ADSC QUANTUM 315r		2017-06-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97918	APS	19-ID

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	1.7	36.96	99.4	15.8	6.9		68713

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	1.7	1.73

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	PDB entries 4GHL & 1TZI	1.7	36.96	61776	3147	93.83	0.1976	0.1958	0.2047	0.233	0.2382	RANDOM	20.163

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]
-0.29			0.07		0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.385
r_dihedral_angle_3_deg	12.859
r_dihedral_angle_4_deg	12.759
r_dihedral_angle_1_deg	7.153
r_angle_refined_deg	1.307
r_angle_other_deg	1.298
r_chiral_restr	0.053
r_bond_other_d	0.007
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4219
Nucleic Acid Atoms
Solvent Atoms	625
Heterogen Atoms	7

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing