9Q9Q | pdb_00009q9q

TRIM21 PRYSPRY bound to compound 38

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2IWG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	291.15	30% PEG 10000, 0.1 M TRIS HCl pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.905	α = 90
b = 61.067	β = 99.152
c = 67.269	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 EIGER2 X 16M		2021-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.979	Diamond	I04

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	2.25	44.993	86.2	0.97	4.5	2.8		14735

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	2.25	2.32			0.449

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.253	44.993	14713	715	85.935	0.255	0.2516	0.2448	0.3251	0.3161	35.665

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]
1.474		0.59	-2.177		0.487

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.109
r_dihedral_angle_3_deg	21.836
r_dihedral_angle_4_deg	17.637
r_dihedral_angle_1_deg	9.295
r_lrange_it	8.534
r_lrange_other	8.532
r_mcangle_other	5.46
r_mcangle_it	5.457
r_scangle_it	4.768
r_scangle_other	4.767
r_mcbond_it	3.351
r_mcbond_other	3.336
r_scbond_it	2.872
r_scbond_other	2.871
r_angle_refined_deg	1.72
r_angle_other_deg	1.184
r_nbd_refined	0.225
r_nbd_other	0.213
r_xyhbond_nbd_refined	0.208
r_symmetry_nbd_other	0.204
r_nbtor_refined	0.189
r_symmetry_nbd_refined	0.106
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.066
r_symmetry_xyhbond_nbd_other	0.028
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2950
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	72

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing