5QIS | pdb_00005qis

Covalent fragment group deposition -- Crystal Structure of OUTB2 in complex with PCM-0102500

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 = 47.421	α = 90
b = 58.75	β = 116.36
c = 50.099	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	1.53	29.37	99.8	0.048	0.057	0.031	0.999	14.5	3.4		37282

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	1.53	1.57	99		0.657	0.779	0.415	0.7		3.4	2718

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	1.53	29.39	35639	1623	99.8	0.1402	0.1378	0.15	0.1903	0.19	RANDOM	22.078

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]
0.1		-0.07	0.08		-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.113
r_sphericity_free	25.949
r_dihedral_angle_4_deg	21.133
r_sphericity_bonded	14.292
r_dihedral_angle_3_deg	12.526
r_dihedral_angle_1_deg	6.187
r_rigid_bond_restr	3.756
r_mcangle_it	3.413
r_mcbond_it	2.802
r_mcbond_other	2.801

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.113
r_sphericity_free	25.949
r_dihedral_angle_4_deg	21.133
r_sphericity_bonded	14.292
r_dihedral_angle_3_deg	12.526
r_dihedral_angle_1_deg	6.187
r_rigid_bond_restr	3.756
r_mcangle_it	3.413
r_mcbond_it	2.802
r_mcbond_other	2.801
r_angle_refined_deg	1.886
r_angle_other_deg	1.156
r_chiral_restr	0.097
r_bond_refined_d	0.018
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1847
Nucleic Acid Atoms
Solvent Atoms	239
Heterogen Atoms	29

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.