5QIT | pdb_00005qit

Covalent fragment group deposition -- Crystal Structure of OUTB2 in complex with PCM-0102821

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
2.34	47.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.289	α = 90
b = 58.436	β = 115.87
c = 49.713	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	1.46	29.22	97.6	0.071	0.084	0.045	0.998	10.2	3.4		41348

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	1.46	1.5	95.2		0.677	0.818	0.452	0.65		3.2	2978

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	1TFF	1.46	29.24	39512	1813	97.38	0.1439	0.1415	0.1412	0.1946	0.1937	RANDOM	17.96

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]
0.31			-0.04		-0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.588
r_sphericity_free	27.478
r_dihedral_angle_4_deg	21.424
r_sphericity_bonded	14.108
r_dihedral_angle_3_deg	12.284
r_dihedral_angle_1_deg	7.168
r_rigid_bond_restr	3.317
r_mcangle_it	3.223
r_mcbond_it	2.571
r_mcbond_other	2.522

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.588
r_sphericity_free	27.478
r_dihedral_angle_4_deg	21.424
r_sphericity_bonded	14.108
r_dihedral_angle_3_deg	12.284
r_dihedral_angle_1_deg	7.168
r_rigid_bond_restr	3.317
r_mcangle_it	3.223
r_mcbond_it	2.571
r_mcbond_other	2.522
r_angle_refined_deg	2.202
r_angle_other_deg	2.036
r_chiral_restr	0.095
r_bond_refined_d	0.018
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1843
Nucleic Acid Atoms
Solvent Atoms	207
Heterogen Atoms	31

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 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.