2GMK | pdb_00002gmk

Crystal structure of onconase double mutant with spontaneously-assembled (AMP) 4 stack

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	PROTEIN SOLUTION (21.4 MG/ML PROTEIN) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (30.6% MEPEG 2K, 0.050 M AMP, 0.090 M BisTris pH 6.5) Crystals cryo-protected with the well solution supplemented with 5% ethylene glycol, vapor diffusion, hanging drop, temperature 293K, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 28.994	α = 90
b = 52.112	β = 90
c = 66.142	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	BRUKER PROTEUM-R	MONTEL OPTICS	2006-01-27		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.5418

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	66.142	99.9	0.0542	40.66	26.59		12645

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)
	1.65	1.7	99.6		0.6625	3.32	5.07	1046

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-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 1onc	1.65	40.927	12597	612	99.889	0.168	0.1653	0.17	0.2173	0.22	RANDOM	19.346

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]
-0.717			-0.534		1.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.399
r_dihedral_angle_3_deg	12.735
r_dihedral_angle_1_deg	6.904
r_scangle_it	4.723
r_dihedral_angle_4_deg	3.664
r_scbond_it	3.193
r_mcangle_it	1.924
r_angle_refined_deg	1.718
r_mcbond_it	1.064
r_nbtor_refined	0.301

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.399
r_dihedral_angle_3_deg	12.735
r_dihedral_angle_1_deg	6.904
r_scangle_it	4.723
r_dihedral_angle_4_deg	3.664
r_scbond_it	3.193
r_mcangle_it	1.924
r_angle_refined_deg	1.718
r_mcbond_it	1.064
r_nbtor_refined	0.301
r_nbd_refined	0.198
r_symmetry_vdw_refined	0.18
r_xyhbond_nbd_refined	0.124
r_symmetry_hbond_refined	0.114
r_chiral_restr	0.104
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	859
Nucleic Acid Atoms
Solvent Atoms	196
Heterogen Atoms	92

Software

Software
Software Name	Purpose
SAINT	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.