5QIX

Covalent fragment group deposition -- Crystal Structure of OUTB2 in complex with PCM-0103007

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	16% PEG4K, 0.1M HEPES pH 7.0, 8% 2-propanol, 5 mM DTT

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.554	α = 90
b = 58.334	β = 116.38
c = 50.333	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	100	PIXEL	DECTRIS PILATUS 6M		2017-06-28		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92819	Diamond	I04-1

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	1.39	29.17	98.4	0.074	0.088	0.047	0.997	9.1	3.3		48731

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	1.39	1.43	96.3		0.621	0.773	0.453	0.629		2.8	3505

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	1TFF	1.39	29.18	46522	2189	98.13	0.1494	0.1471	0.1978	RANDOM	14.222

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]
-0.04		-0.09	0.4		-0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	32.912
r_dihedral_angle_2_deg	32.362
r_dihedral_angle_4_deg	19.625
r_sphericity_bonded	18.967
r_dihedral_angle_3_deg	12.544
r_rigid_bond_restr	12.475
r_dihedral_angle_1_deg	12.456
r_mcangle_it	2.819
r_mcbond_it	2.206
r_mcbond_other	2.205

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	32.912
r_dihedral_angle_2_deg	32.362
r_dihedral_angle_4_deg	19.625
r_sphericity_bonded	18.967
r_dihedral_angle_3_deg	12.544
r_rigid_bond_restr	12.475
r_dihedral_angle_1_deg	12.456
r_mcangle_it	2.819
r_mcbond_it	2.206
r_mcbond_other	2.205
r_angle_refined_deg	2.084
r_angle_other_deg	1.113
r_chiral_restr	0.103
r_bond_refined_d	0.02
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1820
Nucleic Acid Atoms
Solvent Atoms	256
Heterogen Atoms	44

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.