9HT1 | pdb_00009ht1

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		283.15	Morpheus 0.1 Amino acids, 0.1M Buffer system 3 pH 8.5 50% v/v precipitant Mix 1

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.989	α = 90
b = 79.035	β = 90
c = 84.194	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		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	1.94	57.62	99.95	0.142	0.1478	0.04064	0.998	12.97	13.2		21437

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	1.94	2.009	100		1.099	1.142	0.3088	0.778		13.5

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	1.94	57.62	20397	1033	99.95	0.17995	0.17783	0.1903	0.22164	0.2302	RANDOM	29.793

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]
-1.32			1.13		0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.755
r_long_range_B_other	10.642
r_long_range_B_refined	10.62
r_scangle_other	8.834
r_scbond_it	6.299
r_scbond_other	6.298
r_dihedral_angle_1_deg	5.953
r_mcangle_it	3.846
r_mcangle_other	3.844
r_mcbond_it	3.301

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.755
r_long_range_B_other	10.642
r_long_range_B_refined	10.62
r_scangle_other	8.834
r_scbond_it	6.299
r_scbond_other	6.298
r_dihedral_angle_1_deg	5.953
r_mcangle_it	3.846
r_mcangle_other	3.844
r_mcbond_it	3.301
r_mcbond_other	3.277
r_angle_refined_deg	1.406
r_angle_other_deg	0.5
r_chiral_restr	0.07
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2124
Nucleic Acid Atoms
Solvent Atoms	192
Heterogen Atoms	46

Software

Software
Software Name	Purpose
REFMAC	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.