4BTX | pdb_00004btx

Crystal structure of human vascular adhesion protein-1 in complex with pyridazinone inhibitors

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1US1	PDB ENTRY 1US1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				0.6-0.75 M NA/K TARTRATE, 0.2 M NACL, 0.1 M HEPES PH 7.4-7.6

Crystal Properties
Matthews coefficient	Solvent content
4.91	74.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 226.35	α = 90
b = 226.35	β = 90
c = 217.226	γ = 120

Symmetry
Space Group	P 65 2 2

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		2011-05-05	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	2.78	50	99.9	0.18	19.4	7		62917		2.36

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.78	2.83	99.5			5.4

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 1US1	2.78	49.05	62917	3319	80.41	0.18346	0.18065	0.18	0.23679	0.23	RANDOM	39.991

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]
0.66	0.66		0.66		-2.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.837
r_dihedral_angle_4_deg	20.278
r_dihedral_angle_3_deg	19.573
r_dihedral_angle_1_deg	8.616
r_mcangle_it	4.403
r_scbond_it	2.714
r_mcbond_it	2.63
r_mcbond_other	2.621
r_angle_refined_deg	1.73
r_angle_other_deg	0.858
r_chiral_restr	0.09
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001
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_mcangle_other
r_scbond_other
r_scangle_it
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	11156
Nucleic Acid Atoms
Solvent Atoms	292
Heterogen Atoms	238

Software

Software
Software Name	Purpose
HKL	data reduction
HKL	data scaling
CCP4	phasing
MOLREP	phasing
REFMAC	refinement