6Z4N | pdb_00006z4n

CRYSTAL STRUCTURE OF OASS COMPLEXED WITH UPAR INHIBITOR

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OAS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	Drops contained 1 uL of 20 mg/mL StOASS-A mixed with 1 uL of reservoir solution containing 30-31% (w/v) PEG4000, 130-180 mM Li2SO4 (Fluka), 100 mM Tris base pH = 7.0.

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.261	α = 90
b = 96.275	β = 90
c = 140.835	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	100	PIXEL	DECTRIS PILATUS 2M		2018-04-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	1	ELETTRA	5.2R

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	1.2	46.648	94.35	0.0286	0.04044	0.0286	0.999	10.89	1.9		214538			10.08

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	1.2	1.243	65.85		0.5601	0.7921	0.5601	0.569	0.72	1.5

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1OAS	1.2	46.648	214536	10659	94.96	0.155	0.1542	0.16	0.1787	0.18	16.357

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]
-1.685			2.071		-0.387

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.557
r_dihedral_angle_4_deg	15.49
r_dihedral_angle_3_deg	12.585
r_dihedral_angle_1_deg	6.262
r_rigid_bond_restr	6.148
r_lrange_it	3.268
r_lrange_other	2.974
r_scangle_it	2.674
r_scangle_other	2.674
r_scbond_it	2.324
r_scbond_other	2.316
r_chiral_restr_other	1.931
r_mcangle_other	1.89
r_mcangle_it	1.889
r_angle_refined_deg	1.874
r_angle_other_deg	1.574
r_mcbond_it	1.457
r_mcbond_other	1.455
r_symmetry_xyhbond_nbd_other	0.609
r_nbd_refined	0.221
r_symmetry_nbd_other	0.179
r_nbd_other	0.173
r_nbtor_refined	0.169
r_xyhbond_nbd_refined	0.168
r_symmetry_xyhbond_nbd_refined	0.116
r_chiral_restr	0.105
r_ncsr_local_group_1	0.1
r_symmetry_nbtor_other	0.084
r_symmetry_nbd_refined	0.074
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_gen_planes_other	0.004
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4787
Nucleic Acid Atoms
Solvent Atoms	869
Heterogen Atoms	99

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing