6WS0 | pdb_00006ws0

Rational drug design of phenazopyridine derivatives as novel inhibitors of Rev1-CT

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3VU7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	162 mM triammonium citrate and 18% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
1.73	28.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.376	α = 90
b = 69.376	β = 90
c = 106.391	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	280	PIXEL	DECTRIS EIGER2 X 9M		2019-06-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	0.97934	NSLS-II	17-ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	2.238	29.073	99.4	0.107	0.997	12.9	9		14749

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	2.238	2.31			0.774

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	3vu7	2.24	29.07	14717	771	99.439	0.205	0.204	0.21	0.221	0.23	47.319

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]
-0.587	-0.293		-0.587		1.904

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.962
r_dihedral_angle_4_deg	19.043
r_dihedral_angle_3_deg	16.738
r_lrange_it	11.136
r_lrange_other	11.135
r_scangle_it	8.343
r_scangle_other	8.341
r_dihedral_angle_1_deg	8.011
r_mcangle_it	6.951
r_mcangle_other	6.95
r_scbond_it	5.337
r_scbond_other	5.335
r_mcbond_it	4.653
r_mcbond_other	4.647
r_angle_other_deg	2.289
r_angle_refined_deg	1.824
r_nbd_other	0.253
r_symmetry_nbd_other	0.225
r_nbd_refined	0.222
r_symmetry_xyhbond_nbd_refined	0.194
r_nbtor_refined	0.173
r_symmetry_nbd_refined	0.153
r_xyhbond_nbd_refined	0.147
r_chiral_restr	0.087
r_symmetry_nbtor_other	0.076
r_bond_other_d	0.034
r_symmetry_xyhbond_nbd_other	0.016
r_gen_planes_other	0.011
r_bond_refined_d	0.01
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2470
Nucleic Acid Atoms
Solvent Atoms	11
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
MOLREP	phasing