3C05 | pdb_00003c05

Crystal structure of Acostatin from Agkistrodon Contortrix Contortrix

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1J2L	PDB ENTRY 1J2L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5		1.8M AMMONIUM SULFATE, 0.1M TRIS-HCL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 8.50

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.449	α = 90
b = 59.808	β = 90
c = 121.307	γ = 90

Symmetry
Space Group	P 21 21 21

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		2002-10-19	M	SINGLE WAVELENGTH
2	1		CCD	ADSC QUANTUM 210
3	1		IMAGE PLATE	MAR scanner 345 mm plate
4	1		IMAGE PLATE	MAR scanner 345 mm plate

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2		ALS	5.0.2
2	SYNCHROTRON	NSLS BEAMLINE X6A		NSLS	X6A
3	SYNCHROTRON	SSRL BEAMLINE BL9-1		SSRL	BL9-1
4	SYNCHROTRON	SSRL BEAMLINE BL7-1		SSRL	BL7-1

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	1.7	20	98.8	0.044	13.1	13.7		30457

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)
	1.7	1.76	90.9		0.156	8.5	9.2

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	PDB ENTRY 1J2L	1.7	19.67	30750	28838	1543	98.8	0.188	0.186	0.19	0.215	0.22	RANDOM	26.54

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]
-0.01			-0.01		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.829
r_dihedral_angle_4_deg	13.305
r_dihedral_angle_3_deg	11.962
r_dihedral_angle_1_deg	5.883
r_scangle_it	4.755
r_scbond_it	2.959
r_mcangle_it	1.851
r_angle_refined_deg	1.329
r_mcbond_it	1.16
r_nbtor_refined	0.295
r_nbd_refined	0.189
r_symmetry_vdw_refined	0.153
r_symmetry_hbond_refined	0.141
r_xyhbond_nbd_refined	0.136
r_chiral_restr	0.097
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1686
Nucleic Acid Atoms
Solvent Atoms	303
Heterogen Atoms	15

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing