9RXX | pdb_00009rxx

Ty1 Prime Retrotransposon Capsid C-Terminal Domain, F323S

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Related entry (Ty1 Prime Retrotransposon Capsid C-Terminal Domain, wt) was used as a search model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	150 nL protein (70mg/ml (6.33mM) in 20 mM Tris pH 8.5, 150mM NaCl, 1mM TCEP) mixed with 50 nL well solution (0.2M NH4Cl, 20% PEG6K, 0.1M Tris pH8)

Crystal Properties
Matthews coefficient	Solvent content
1.88	34.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.232	α = 90
b = 52.753	β = 108.538
c = 45.959	γ = 90

Symmetry
Space Group	P 1 21 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 PILATUS 6M		2021-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.99990	Diamond	I24

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	1.616	43.58	71.4	0.087	0.03	0.997	10.81	7.8		15110			38.49

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	1.616	1.789	13.61		1.073	0.465	0.5964

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	1.616	43.575	15109	759	71.383	0.224	0.2221	0.2682	0.3169	Random selection	36.031

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]
1.126		0.263	-1.735		0.353

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.054
r_dihedral_angle_3_deg	15.367
r_dihedral_angle_6_deg	13.976
r_lrange_it	6.397
r_lrange_other	6.389
r_scangle_it	4.856
r_scangle_other	4.854
r_dihedral_angle_1_deg	4.568
r_mcangle_other	3.774
r_mcangle_it	3.773
r_scbond_it	3.131
r_scbond_other	3.129
r_mcbond_it	2.397
r_mcbond_other	2.394
r_angle_refined_deg	1.262
r_angle_other_deg	0.398
r_nbd_other	0.345
r_symmetry_nbd_refined	0.309
r_nbd_refined	0.238
r_symmetry_nbd_other	0.197
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.133
r_symmetry_xyhbond_nbd_refined	0.128
r_ncsr_local_group_1	0.086
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.058
r_bond_refined_d	0.006
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	1379
Nucleic Acid Atoms
Solvent Atoms	32
Heterogen Atoms

Software

Software
Software Name	Purpose
XDS	data reduction
Aimless	data scaling
STARANISO	data scaling
PHASER	phasing
BUCCANEER	model building
Coot	model building
REFMAC	refinement