9HT2 | pdb_00009ht2

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	8.5	283.15	Morpheus 0.09 M Halogens, 0.1M Buffer system 3 pH 8.5 50% v/v precipitant mix 1

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.353	α = 90
b = 39.553	β = 105.492
c = 55.861	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	120	PIXEL	DECTRIS EIGER X 16M		2022-09-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.977020	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	1.42	26.93	95.93	0.07624	0.08237	0.03085	0.998	13.07	7.1		23321

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	1.42	1.471	93.4		0.6479	0.6998	0.262	0.838	2.6	7

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	1.42	26.93	22157	1215	96	0.1725	0.17173	0.1775	0.18634	0.1944	RANDOM	24.278

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]
-0.35		0.54	-1.18		1.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.305
r_long_range_B_other	9.651
r_long_range_B_refined	9.59
r_scangle_other	8.645
r_scbond_it	7.543
r_scbond_other	7.541
r_dihedral_angle_1_deg	5.586
r_mcbond_it	4.464
r_mcangle_it	4.418
r_mcangle_other	4.417

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.305
r_long_range_B_other	9.651
r_long_range_B_refined	9.59
r_scangle_other	8.645
r_scbond_it	7.543
r_scbond_other	7.541
r_dihedral_angle_1_deg	5.586
r_mcbond_it	4.464
r_mcangle_it	4.418
r_mcangle_other	4.417
r_mcbond_other	4.325
r_angle_refined_deg	1.259
r_angle_other_deg	0.451
r_chiral_restr	0.052
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
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	156
Heterogen Atoms	36

Software

Software
Software Name	Purpose
PHENIX	refinement
PDB-REDO	refinement
MxCuBE	data collection
autoPROC	data reduction
autoPROC	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.