7B6A | pdb_00007b6a

BK Polyomavirus VP1 pentamer core (residues 30-299)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4MJ0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	298	10% PEG 3350, 0.2 M NaJ, 0.1 M bis-tris pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 138.622	α = 90
b = 149.719	β = 90
c = 65.488	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	PIXEL	DECTRIS PILATUS 2M		2017-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE F1	0.976800	CHESS	F1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim 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	1.44	50	99.9	0.029	0.999	16.4	13.2		245801			18.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.44	1.49	99.8		0.562	0.62	1.3	11.8

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	4mj0	1.44	50	245801	4820	99.97	0.163	0.1621	0.17	0.1858	0.19	22.343

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]
-0.144			-0.339		0.484

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.905
r_dihedral_angle_4_deg	21.872
r_dihedral_angle_3_deg	12.322
r_dihedral_angle_1_deg	7.409
r_lrange_it	6.754
r_lrange_other	6.754
r_scangle_it	2.996
r_scangle_other	2.996
r_mcangle_it	2.215
r_mcangle_other	2.214
r_scbond_it	1.988
r_scbond_other	1.988
r_angle_refined_deg	1.851
r_angle_other_deg	1.534
r_mcbond_it	1.321
r_mcbond_other	1.321
r_symmetry_nbd_refined	0.371
r_nbd_other	0.276
r_symmetry_xyhbond_nbd_refined	0.255
r_nbd_refined	0.223
r_xyhbond_nbd_refined	0.208
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.169
r_symmetry_metal_ion_refined	0.168
r_metal_ion_refined	0.16
r_ncsr_local_group_4	0.12
r_ncsr_local_group_10	0.112
r_ncsr_local_group_9	0.106
r_ncsr_local_group_1	0.103
r_ncsr_local_group_2	0.099
r_ncsr_local_group_3	0.099
r_ncsr_local_group_5	0.098
r_ncsr_local_group_6	0.098
r_ncsr_local_group_8	0.098
r_chiral_restr	0.091
r_ncsr_local_group_7	0.085
r_symmetry_nbtor_other	0.084
r_symmetry_xyhbond_nbd_other	0.076
r_bond_refined_d	0.015
r_gen_planes_refined	0.011
r_gen_planes_other	0.004
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10145
Nucleic Acid Atoms
Solvent Atoms	1523
Heterogen Atoms	79

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing