9RXW | pdb_00009rxw

Ty1 Prime Retrotransposon Capsid C-Terminal Domain, wt

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7NLH	Polyalanine model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	293	150 nL protein (12 mg/ml (1.067mM) in 20 mM Tris pH 8.5, 150mM NaCl, 1mM TCEP) mixed with 50 nL well solution (0.2M NaCl, 10% PEG3K, 0.1M Na Phos Citrate pH4.2)

Crystal Properties
Matthews coefficient	Solvent content
2	38.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.593	α = 101.641
b = 34.332	β = 96.351
c = 45.333	γ = 109.279

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	100	PIXEL	DECTRIS EIGER2 XE 16M		2020-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.6	43.59	82.6	0.067	0.034	0.999	20	3.4		18863			20.42

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.63	31.26		1.524	0.833	0.492		3.1

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.6	43.577	18833	978	82.496	0.181	0.1798	0.2022	0.1929	Random selection	23.523

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]
0.695	-0.722	-1.663	0.886	-0.925	0.062

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.37
r_dihedral_angle_6_deg	14.9
r_dihedral_angle_3_deg	14.425
r_lrange_it	6.442
r_lrange_other	6.411
r_dihedral_angle_1_deg	4.987
r_scangle_it	4.082
r_scangle_other	4.08
r_mcangle_other	2.929
r_mcangle_it	2.928
r_scbond_it	2.759
r_scbond_other	2.757
r_mcbond_it	1.786
r_mcbond_other	1.785
r_angle_refined_deg	1.375
r_angle_other_deg	0.489
r_symmetry_xyhbond_nbd_other	0.254
r_nbd_refined	0.239
r_symmetry_nbd_other	0.194
r_symmetry_nbd_refined	0.192
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.141
r_nbd_other	0.138
r_ncsr_local_group_1	0.099
r_symmetry_nbtor_other	0.072
r_chiral_restr	0.068
r_symmetry_xyhbond_nbd_refined	0.041
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1417
Nucleic Acid Atoms
Solvent Atoms	74
Heterogen Atoms

Software

Software
Software Name	Purpose
xia2	data reduction
DIALS	data reduction
TRUNCATE	data scaling
PHASER	phasing
ARP/wARP	model building
Coot	model building
REFMAC	refinement