6YDR | pdb_00006ydr

Crystal structure of Mengla Virus VP30 C-terminal domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5T3W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2M Ammonium Sulfate , 0.1M Sodium, Acetate pH4.6, 25% PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.062	α = 90
b = 73.062	β = 90
c = 53.459	γ = 120

Symmetry
Space Group	P 32 1 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 PILATUS3 6M		2019-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.979	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.34	40.87	99.9	0.06541	0.07254	0.03027	0.993	16.27	5.4		36367

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.344	1.392			0.4376	0.4909	0.2158	0.852	2.82

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	5T3W	1.34	40.87	34575	1792	99.88	0.12848	0.12705	0.14	0.15496	0.16	RANDOM	23.282

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]
-0.5	-0.25		-0.5		1.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.228
r_dihedral_angle_4_deg	13.829
r_dihedral_angle_3_deg	10.737
r_scbond_it	9.982
r_scbond_other	9.927
r_scangle_other	9.181
r_rigid_bond_restr	6.14
r_long_range_B_refined	5.003
r_dihedral_angle_1_deg	4.765
r_long_range_B_other	4.532
r_mcangle_other	2.488
r_mcangle_it	2.472
r_mcbond_it	2.246
r_mcbond_other	1.994
r_angle_refined_deg	1.325
r_angle_other_deg	1.288
r_chiral_restr	0.094
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1008
Nucleic Acid Atoms
Solvent Atoms	152
Heterogen Atoms	11

Software

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