9Q9R | pdb_00009q9r

TRIM21 PRYSPRY bound to compound 209

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	9.6	291.15	20% (w/v) PEG-8000, 0.1M CHES pH 9.5 (final pH 9.6)

Crystal Properties
Matthews coefficient	Solvent content
1.95	37.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.068	α = 90
b = 60.827	β = 112.543
c = 42.223	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		2023-05-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.619	Diamond	I24

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	2.33	30.432	99.6	0.955	5.4	3.5		7445

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	2.33	2.41			0.296

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	2.331	30.432	7432	363	99.478	0.227	0.2224	0.234	0.3137	0.324	35.966

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]
-1.762		1.354	0.154		0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.979
r_dihedral_angle_3_deg	20.192
r_dihedral_angle_4_deg	14.656
r_dihedral_angle_1_deg	8.968
r_lrange_other	6.929
r_lrange_it	6.927
r_mcangle_it	4.023
r_mcangle_other	4.021
r_scangle_it	3.965
r_scangle_other	3.964
r_mcbond_it	2.41
r_mcbond_other	2.402
r_scbond_it	2.397
r_scbond_other	2.396
r_angle_refined_deg	1.444
r_angle_other_deg	1.144
r_nbd_other	0.238
r_nbd_refined	0.224
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.169
r_symmetry_nbd_refined	0.082
r_symmetry_nbtor_other	0.079
r_symmetry_xyhbond_nbd_refined	0.079
r_chiral_restr	0.053
r_symmetry_xyhbond_nbd_other	0.013
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1475
Nucleic Acid Atoms
Solvent Atoms	11
Heterogen Atoms	44

Software

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