2DOI | pdb_00002doi

The X-ray crystallographic structure of the angiogenesis inhibitor, angiostatin, bound to a peptide from the group A streptococcus protein PAM

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DOH	PDB ID 2DOH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	20% PEG 8000, 0.1M potassium phophate (dihydrate), 5% dioxane, soaked in 5mM Pt(C5H5N)2Cl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.16	61.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.467	α = 90
b = 58.467	β = 90
c = 389.146	γ = 120

Symmetry
Space Group	P 61

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD	MAR CCD 165 mm		2003-07-15	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 5ID-B	1.0719	APS	5ID-B

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	2.8	50	85.1	0.086	11.5			15828		3

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	2.8	2.9	22.2		0.507			410

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-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 ID 2DOH	3.1	20	13107	675	97.01	0.206	0.202	0.202	0.2	0.296	0.25	RANDOM	35.457

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]
1.78	0.89		1.78		-2.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.818
r_scangle_it	32.957
r_scbond_it	30.591
r_dihedral_angle_3_deg	25.161
r_dihedral_angle_4_deg	23.7
r_mcangle_it	19.526
r_mcbond_it	15.827
r_dihedral_angle_1_deg	9.614
r_angle_refined_deg	2.593
r_symmetry_hbond_refined	0.457

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.818
r_scangle_it	32.957
r_scbond_it	30.591
r_dihedral_angle_3_deg	25.161
r_dihedral_angle_4_deg	23.7
r_mcangle_it	19.526
r_mcbond_it	15.827
r_dihedral_angle_1_deg	9.614
r_angle_refined_deg	2.593
r_symmetry_hbond_refined	0.457
r_nbd_refined	0.38
r_nbtor_refined	0.372
r_symmetry_vdw_refined	0.358
r_xyhbond_nbd_refined	0.335
r_chiral_restr	0.155
r_bond_refined_d	0.023
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3064
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.