6WS5 | pdb_00006ws5

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 Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.019	α = 90
b = 73.023	β = 90
c = 85.554	γ = 90

Symmetry
Space Group	P 21 21 21

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 EIGER X 9M		2019-09-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	.9201	NSLS-II	17-ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.47	29.508	99.6	0.067	0.075	0.028	0.999	13.7	6.4		11712

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.47	2.57			0.784	0.857	0.47	0.823	2

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	2.472	29.508	11673	620	99.497	0.203	0.2014	0.21	0.2375	0.24	70

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]
3.385			0.161		-3.546

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.572
r_lrange_other	19.498
r_lrange_it	19.497
r_dihedral_angle_3_deg	18.461
r_dihedral_angle_4_deg	17.527
r_scangle_it	16.702
r_scangle_other	16.698
r_mcangle_it	13.921
r_mcangle_other	13.918
r_scbond_it	12.315
r_scbond_other	12.311
r_mcbond_it	10.496
r_mcbond_other	10.488
r_dihedral_angle_1_deg	8.771
r_angle_other_deg	2.344
r_angle_refined_deg	1.924
r_nbd_other	0.291
r_symmetry_nbd_refined	0.27
r_symmetry_xyhbond_nbd_refined	0.251
r_nbd_refined	0.236
r_symmetry_nbd_other	0.23
r_nbtor_refined	0.169
r_xyhbond_nbd_refined	0.145
r_symmetry_xyhbond_nbd_other	0.112
r_chiral_restr	0.097
r_symmetry_nbtor_other	0.078
r_bond_other_d	0.034
r_bond_refined_d	0.014
r_gen_planes_other	0.011
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2546
Nucleic Acid Atoms
Solvent Atoms	1
Heterogen Atoms	18

Software

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