8DEA | pdb_00008dea

Scaffold Hopping via Ring Opening Enables Identification of Acyclic Compounds as New Complement Factor D Inhibitors

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DIC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.8	293	peg4k 25% , 0.1M MES 5.8 buffer

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.898	α = 90
b = 73.032	β = 90
c = 240.864	γ = 90

Symmetry
Space Group	P 2 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	170	PIXEL	DECTRIS PILATUS 200K		2021-05-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.2	50	74.5	0.15	0.311	0.771	5.4	3.2		36438

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	2.2	2.28	46.1		0.771		1.6

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	1dic	2.214	46.46	34591	1694	85.164	0.229	0.225	0.23	0.2998	0.3	33.495

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]
-0.048			0.06		-0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	19.685
r_dihedral_angle_3_deg	16.172
r_dihedral_angle_6_deg	14.435
r_dihedral_angle_1_deg	7.637
r_lrange_it	7.311
r_lrange_other	7.307
r_mcangle_other	4.261
r_mcangle_it	4.26
r_scangle_it	4.219
r_scangle_other	4.219
r_mcbond_it	2.762
r_mcbond_other	2.762
r_scbond_it	2.756
r_scbond_other	2.756
r_angle_refined_deg	1.372
r_chiral_restr_other	1.007
r_angle_other_deg	0.533
r_symmetry_xyhbond_nbd_refined	0.343
r_symmetry_nbd_refined	0.229
r_nbd_other	0.229
r_nbd_refined	0.217
r_symmetry_nbd_other	0.199
r_nbtor_refined	0.163
r_xyhbond_nbd_refined	0.153
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.056
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6484
Nucleic Acid Atoms
Solvent Atoms	84
Heterogen Atoms	120

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
SCALEPACK	data scaling
PHASER	phasing