1US1 | pdb_00001us1

Crystal structure of human vascular adhesion protein-1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PU4	PDB ENTRY 1PU4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8		pH 8.00

Crystal Properties
Matthews coefficient	Solvent content
4.6	73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 226.099	α = 90
b = 226.099	β = 90
c = 223.004	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	MARRESEARCH		2003-09-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1		ESRF	ID14-1

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	2.9	20	93.3	0.121	19	10.4		69536

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	2.9	3	95.3		0.474	6.4	10.4

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 1PU4	2.9	19.96	69536	3476	93.3	0.242	0.241	0.22	0.267	0.25	RANDOM	41.04

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]
-5.68	-2.84		-5.68		8.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	8.822
r_scangle_it	2.705
r_angle_refined_deg	1.891
r_scbond_it	1.571
r_mcangle_it	1.041
r_angle_other_deg	0.99
r_mcbond_it	0.539
r_symmetry_vdw_refined	0.339
r_nbd_other	0.234
r_symmetry_vdw_other	0.228
r_nbd_refined	0.211
r_symmetry_hbond_refined	0.188
r_xyhbond_nbd_refined	0.177
r_chiral_restr	0.1
r_nbtor_other	0.094
r_bond_refined_d	0.02
r_gen_planes_refined	0.007
r_gen_planes_other	0.005
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
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	11063
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	90

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling