2AIP

Crystal structure of native protein C activator from the venom of copperhead snake Agkistrodon contortrix contortrix

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BQY	PDB entry 1BQY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	293	ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.867	α = 90
b = 63.295	β = 99.8
c = 48.237	γ = 90

Symmetry
Space Group	C 1 2 1

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		2005-05-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE D03B-MX1	1.438	LNLS	D03B-MX1

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	1.65	19.03	99.8	0.09				28664	2.5	2.5

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	1.65	1.71	99.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1BQY	1.65	19.03	2.5	27223	1440	99.49	0.1743	0.17086	0.16949	0.19692	RANDOM	21.121

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.602
r_dihedral_angle_4_deg	18.61
r_dihedral_angle_3_deg	12.548
r_dihedral_angle_1_deg	6.219
r_scangle_it	2.999
r_scbond_it	2.03
r_angle_refined_deg	1.493
r_mcangle_it	1.393
r_mcbond_it	0.802
r_nbtor_refined	0.323

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.602
r_dihedral_angle_4_deg	18.61
r_dihedral_angle_3_deg	12.548
r_dihedral_angle_1_deg	6.219
r_scangle_it	2.999
r_scbond_it	2.03
r_angle_refined_deg	1.493
r_mcangle_it	1.393
r_mcbond_it	0.802
r_nbtor_refined	0.323
r_nbd_refined	0.217
r_symmetry_hbond_refined	0.2
r_symmetry_vdw_refined	0.195
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.097
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1757
Nucleic Acid Atoms
Solvent Atoms	183
Heterogen Atoms	67

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

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.