1PU4 | pdb_00001pu4

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	1KSI	PDB ENTRY 1KSI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	298	potassium/sodium tartrate, imidazole, sodium chloride, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
4.75	74.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 225.916	α = 90
b = 225.916	β = 90
c = 218.668	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		2002-10-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.8110	EMBL/DESY, HAMBURG	X11

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	3.2	20	95.9	0.02	13.2	14.1		52367			26.7

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	3.2	3.3	97.2		0.464	6	13.5	4588

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 1KSI	3.2	20	52364	49745	2619	96.36	0.21883	0.21883	0.21699	0.19	0.25364	0.23	RANDOM	28.543

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]
-3.66	-1.83		-3.66		5.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	8.974
r_scangle_it	2.339
r_angle_refined_deg	1.771
r_scbond_it	1.331
r_angle_other_deg	1.086
r_mcangle_it	0.961
r_mcbond_it	0.499
r_symmetry_vdw_other	0.275
r_nbd_other	0.236
r_symmetry_vdw_refined	0.228
r_symmetry_hbond_refined	0.211
r_nbd_refined	0.209
r_xyhbond_nbd_refined	0.175
r_nbtor_other	0.097
r_chiral_restr	0.095
r_bond_refined_d	0.018
r_gen_planes_refined	0.006
r_gen_planes_other	0.004
r_bond_other_d	0.003
r_dihedral_angle_2_deg
r_xyhbond_nbd_other
r_symmetry_hbond_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 scaling
AMoRE	phasing