8XY3 | pdb_00008xy3

Crystal structure of VARV P1 protein

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8XY1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.2 M Calcium chloride dihydrate, 0.1 M Tris pH 8.0, 20% w/v PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.064	α = 90
b = 153.786	β = 90
c = 132.146	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	PIXEL	DECTRIS PILATUS 6M		2024-01-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.97853	SSRF	BL18U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.2	132.15	100	0.993	11.4	12.6		31040

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	2.2	2.27			0.978

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	8XY1	2.2	66.16	31004	1515	99.932	0.206	0.2038	0.21	0.2408	0.2453	44.245

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]
4.588			-1.884		-2.704

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.833
r_dihedral_angle_4_deg	16.711
r_dihedral_angle_3_deg	14.056
r_lrange_other	8.302
r_lrange_it	8.294
r_scangle_it	6.751
r_scangle_other	6.751
r_dihedral_angle_1_deg	6.285
r_mcangle_it	5.114
r_mcangle_other	5.113
r_scbond_it	4.466
r_scbond_other	4.465
r_mcbond_it	3.584
r_mcbond_other	3.584
r_angle_refined_deg	1.473
r_angle_other_deg	1.322
r_symmetry_nbd_refined	0.257
r_nbd_other	0.215
r_symmetry_xyhbond_nbd_refined	0.213
r_nbd_refined	0.206
r_symmetry_nbd_other	0.177
r_nbtor_refined	0.165
r_xyhbond_nbd_refined	0.158
r_ncsr_local_group_5	0.1
r_ncsr_local_group_4	0.096
r_ncsr_local_group_2	0.088
r_ncsr_local_group_1	0.087
r_ncsr_local_group_3	0.087
r_ncsr_local_group_6	0.083
r_chiral_restr	0.079
r_symmetry_nbtor_other	0.077
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3903
Nucleic Acid Atoms
Solvent Atoms	254
Heterogen Atoms

Software

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