28JD | pdb_000028jd

BKPyV VP1 IN COMPLEX WITH scFv 319C07

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		unpublished

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	9	293.15	10% (w/v) PEG 6,000 100 mM Bicine pH 9.0

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.25	α = 90
b = 151.89	β = 90
c = 164.69	γ = 90

Symmetry
Space Group	P 21 21 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	PIXEL	DECTRIS EIGER X 9M		2025-02-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.987	SOLEIL	PROXIMA 2

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	3.7	111.904	99.9	0.023	1	3.7	8.5		29566

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.77	3.79			0.4	0.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3.726	111.904	29562	1475	99.929	0.249	0.2463	0.2517	0.2941	0.2859	RANDOM	120.484

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]
11.218			-3.154		-8.064

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	15.883
r_lrange_other	15.883
r_dihedral_angle_6_deg	14.106
r_dihedral_angle_3_deg	13.841
r_mcangle_it	9.512
r_mcangle_other	9.512
r_scangle_it	8.882
r_scangle_other	8.882
r_dihedral_angle_1_deg	6.999
r_dihedral_angle_2_deg	6.203
r_mcbond_it	5.783
r_mcbond_other	5.781
r_scbond_it	5.247
r_scbond_other	5.246
r_angle_refined_deg	1.245
r_symmetry_xyhbond_nbd_refined	0.588
r_angle_other_deg	0.468
r_symmetry_nbd_refined	0.323
r_nbd_other	0.302
r_symmetry_xyhbond_nbd_other	0.197
r_symmetry_nbd_other	0.186
r_nbd_refined	0.185
r_nbtor_refined	0.165
r_xyhbond_nbd_refined	0.122
r_ncsr_local_group_1	0.08
r_ncsr_local_group_12	0.079
r_symmetry_nbtor_other	0.078
r_ncsr_local_group_6	0.077
r_ncsr_local_group_11	0.076
r_ncsr_local_group_3	0.074
r_ncsr_local_group_5	0.072
r_ncsr_local_group_2	0.065
r_ncsr_local_group_4	0.063
r_ncsr_local_group_13	0.063
r_chiral_restr	0.062
r_ncsr_local_group_8	0.061
r_ncsr_local_group_10	0.057
r_ncsr_local_group_7	0.056
r_ncsr_local_group_9	0.052
r_ext_dist_refined_b	0.035
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15393
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
XSCALE	data scaling
PHASER	phasing