9Q9O | pdb_00009q9o

TRIM21 PRYSPRY bound to compound 36

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		291.15	20% PEG 4000, 5% iso-Propanol, 0.1 M Na Citrate

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.685	α = 90
b = 74.38	β = 90.103
c = 90.109	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		2021-05-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.99	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	2.46	50.427	83.6	0.978	3	3.1		24473

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	2.46	2.56			0.5

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	2.462	50.427	24450	1243	83.496	0.305	0.3017	0.2762	0.368	0.3459	34.201

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]
-2.923		-0.364	6.421		-3.496

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.004
r_dihedral_angle_3_deg	20.772
r_dihedral_angle_4_deg	15.473
r_lrange_it	10.049
r_lrange_other	10.049
r_dihedral_angle_1_deg	9.052
r_mcangle_it	5.097
r_mcangle_other	5.096
r_scangle_it	4.846
r_scangle_other	4.846
r_mcbond_it	3.085
r_mcbond_other	3.084
r_scbond_it	2.84
r_scbond_other	2.84
r_angle_refined_deg	1.693
r_angle_other_deg	1.227
r_nbd_other	0.256
r_symmetry_nbd_refined	0.253
r_nbd_refined	0.217
r_symmetry_nbd_other	0.196
r_xyhbond_nbd_refined	0.184
r_nbtor_refined	0.18
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.072
r_symmetry_xyhbond_nbd_other	0.025
r_chiral_restr_other	0.014
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	5908
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	156

Software

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