Experiment: 2ONQ

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	293.15	50mM sodium acetate, 20mg/ml protein solution mixed in equal volume of crystallization buffer containing 33% PEG monomethylether, 0.1M calcium chloride, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

Crystal Properties
Matthews coefficient	Solvent content
1.91	35.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.412	α = 90
b = 48.412	β = 90
c = 107.332	γ = 120

Symmetry
Space Group	H 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	IMAGE PLATE	MAR scanner 300 mm plate	mirrors / slits	2005-10-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	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	1.7	39.05	99.4	0.03	27.4	5.6	5583	5583	-3	-3	34.418

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	1.7	1.76	100		0.22	7.1	4.9	532

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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 ENTRY 1PGA	1.7	19	-3	5583	5583	256	99.61	0.206	0.206	0.205	0.22	0.229	0.24	RANDOM	30.162

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]
0.74	0.37		0.74		-1.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	50.219
r_dihedral_angle_3_deg	16.626
r_dihedral_angle_1_deg	8.181
r_scangle_it	6.554
r_scbond_it	5.088
r_mcangle_it	3.437
r_mcbond_it	2.401
r_angle_refined_deg	1.819
r_symmetry_hbond_refined	0.35
r_nbtor_refined	0.298

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	50.219
r_dihedral_angle_3_deg	16.626
r_dihedral_angle_1_deg	8.181
r_scangle_it	6.554
r_scbond_it	5.088
r_mcangle_it	3.437
r_mcbond_it	2.401
r_angle_refined_deg	1.819
r_symmetry_hbond_refined	0.35
r_nbtor_refined	0.298
r_xyhbond_nbd_refined	0.22
r_nbd_refined	0.2
r_symmetry_vdw_refined	0.186
r_chiral_restr	0.122
r_bond_refined_d	0.021
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	446
Nucleic Acid Atoms
Solvent Atoms	34
Heterogen Atoms

Software

Software
Software Name	Purpose
XSCALE	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
XDS	data reduction

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.