3LDM

Crystal structure of aprotinin in complex with sucrose octasulfate: unusual interactions and implication for heparin binding

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	295	100mM sodium acetate pH4.6, 2M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.04	59.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.894	α = 90
b = 92.894	β = 90
c = 159.353	γ = 120

Symmetry
Space Group	P 64 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	ADSC QUANTUM 210			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 4A	1.0	PAL/PLS	4A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.6	50	99.8	0.089	10.7		23745	23698

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.6	2.66	100		0.45

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.6	50	13157	13118	644	99.7	0.206	0.203	0.257	RANDOM	41.093

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]
1.79	0.89		1.79		-2.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_4_deg	25.274
r_dihedral_angle_2_deg	23.553
r_dihedral_angle_3_deg	16.824
r_scangle_it	7.244
r_dihedral_angle_1_deg	6.425
r_scbond_it	4.394
r_mcangle_it	3.602
r_rigid_bond_restr	2.394
r_mcbond_it	1.919
r_angle_refined_deg	1.625

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_4_deg	25.274
r_dihedral_angle_2_deg	23.553
r_dihedral_angle_3_deg	16.824
r_scangle_it	7.244
r_dihedral_angle_1_deg	6.425
r_scbond_it	4.394
r_mcangle_it	3.602
r_rigid_bond_restr	2.394
r_mcbond_it	1.919
r_angle_refined_deg	1.625
r_chiral_restr	0.111
r_bond_refined_d	0.017
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2220
Nucleic Acid Atoms
Solvent Atoms	87
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.