7PA6 | pdb_00007pa6

JC polyomavirus VP1 in complex with scFv 27C11

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3NXG	3NXG, 4KQ3
experimental model	PDB	4KQ3	3NXG, 4KQ3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293.15	100 mM potassium phosphate monohydrate / potassium phosphate dihydrate pH 6.0, 10% (w/v) PEG 8000, 686 mM NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.09	α = 100.913
b = 96.11	β = 93.012
c = 190.41	γ = 113.835

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	PIXEL	DECTRIS PILATUS 2M-F		2016-04-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.99	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	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	1.9	48.5	89.9	0.1	0.99	9.27	3.83		465782

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2.01			1.19	0.5	1.15

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3NXG, 4KQ3	1.9	47.809	465782	23290	97.59	0.185	0.1835	0.19	0.2164	0.22	36.13

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]
1.146	1.239	-0.33	-0.626	-0.557	-0.758

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.253
r_dihedral_angle_4_deg	15.824
r_dihedral_angle_3_deg	13.666
r_lrange_it	8.463
r_lrange_other	8.452
r_dihedral_angle_1_deg	6.74
r_scangle_it	6.373
r_scangle_other	6.373
r_mcangle_it	4.516
r_mcangle_other	4.516
r_scbond_it	4.381
r_scbond_other	4.381
r_mcbond_other	3.249
r_mcbond_it	3.248
r_angle_other_deg	2.36
r_angle_refined_deg	1.604
r_symmetry_nbd_other	0.231
r_nbd_other	0.229
r_nbd_refined	0.195
r_symmetry_nbd_refined	0.185
r_nbtor_refined	0.177
r_symmetry_xyhbond_nbd_refined	0.16
r_xyhbond_nbd_refined	0.143
r_symmetry_xyhbond_nbd_other	0.138
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.073
r_bond_other_d	0.037
r_bond_refined_d	0.01
r_gen_planes_other	0.009
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	37890
Nucleic Acid Atoms
Solvent Atoms	2249
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing