4AQH | pdb_00004aqh

Plasminogen activator inhibitor type-1 in complex with the inhibitor AZ3976

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6		PAI-1 WAS CONCENTRATED TO ABOUT 4 G/L IN A BUFFER CONTAINING 10 MM SODIUM ACETATE PH 5.6, 150 MM SODIUM CHLORIDE AND 1 MM EDTA. AZ3976 WAS DISSOLVED IN DEUTERATED DMSO AND ADDED TO THE PROTEIN SAMPLE TO A FINAL CONCENTRATION OF 0.3 MM. CRYSTALS WERE OBTAINED BY THE HANGING DROP VAPOR DIFFUSION TECHNIQUE: 2.5 UL PROTEIN SAMPLE WAS MIXED WITH 1 UL OF A WELL SOLUTION CONTAINING 2.0 M SODIUM CHLORIDE, 100 MM BIS-TRIS PH 6.8

Crystal Properties
Matthews coefficient	Solvent content
3.2	61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.399	α = 90
b = 119.399	β = 90
c = 99.691	γ = 120

Symmetry
Space Group	P 31

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD		2010-06-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2		ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.4	49.9	100	0.1	16	5.9		62179		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.46	100		0.7	2.4	5.9

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1DVN	2.4	60.01	58169	3163	98.67	0.15867	0.15743	0.1572	0.18138	0.1686	RANDOM	45.905

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]
4.45			4.45		-8.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.198
r_dihedral_angle_4_deg	19.41
r_dihedral_angle_3_deg	17.641
r_dihedral_angle_1_deg	5.464
r_scangle_it	3.793
r_scbond_it	2.358
r_mcangle_it	1.564
r_angle_refined_deg	1.485
r_mcbond_it	0.826
r_chiral_restr	0.099
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9115
Nucleic Acid Atoms
Solvent Atoms	244
Heterogen Atoms	69

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing