9HT0 | pdb_00009ht0

A novel bottom-up approach to find lead-compounds in billion-sized libraries

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4ZC9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		292.15	Morpheus 0.09M Halogens, 0.1M Buffer System 2 pH6.5, 50% v/v Precipitant Mix 2

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.1	α = 90
b = 44.587	β = 90
c = 78.907	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	120	PIXEL	DECTRIS EIGER X 16M		2021-12-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.976260	PETRA III, EMBL c/o DESY	P13 (MX1)

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	1.33	38.85	99.87	0.06058	0.06315	0.01762	0.999	18.97	12.7		29986

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	1.33	1.378	99.46		0.8042	0.837	0.2289	0.913	2.62	12.9

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.33	38.85	28623	1484	99.87	0.18759	0.18654	0.1921	0.20806	0.2181	RANDOM	23.77

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]
2.99			-0.44		-2.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.449
r_long_range_B_refined	7.274
r_long_range_B_other	7.258
r_scangle_other	6.476
r_dihedral_angle_1_deg	5.469
r_scbond_other	5.082
r_scbond_it	5.08
r_mcangle_other	2.286
r_mcangle_it	2.283
r_mcbond_other	1.884

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.449
r_long_range_B_refined	7.274
r_long_range_B_other	7.258
r_scangle_other	6.476
r_dihedral_angle_1_deg	5.469
r_scbond_other	5.082
r_scbond_it	5.08
r_mcangle_other	2.286
r_mcangle_it	2.283
r_mcbond_other	1.884
r_mcbond_it	1.881
r_angle_refined_deg	0.999
r_angle_other_deg	0.392
r_chiral_restr	0.05
r_bond_refined_d	0.006
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1062
Nucleic Acid Atoms
Solvent Atoms	151
Heterogen Atoms	33

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.