Experiment: 3PNK

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OI2	pdb entry 1OI2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	295	20% PEG 8000, 0.1M Sodium Citrate pH 5.6, vapor diffusion, sitting drop, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.833	α = 90
b = 91.507	β = 89.96
c = 73.232	γ = 90

Symmetry
Space Group	P 1 21 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			2008-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.9793	APS	31-ID

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	2.21	49.83	93.3	0.122	9.5	5.2		30618

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	2.21	2.29	81.1		0.457		2.7	2634

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1OI2	2.21	49.83	30579	1561	93	0.1738	0.1719	0.2099	RANDOM	30.6636

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]
-0.19		-0.01	-0.56		0.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.59
r_dihedral_angle_4_deg	20.742
r_dihedral_angle_3_deg	15.709
r_dihedral_angle_1_deg	6.351
r_scangle_it	2.839
r_scbond_it	1.78
r_angle_refined_deg	1.354
r_mcangle_it	1.081
r_mcbond_it	0.635
r_nbtor_refined	0.301

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.59
r_dihedral_angle_4_deg	20.742
r_dihedral_angle_3_deg	15.709
r_dihedral_angle_1_deg	6.351
r_scangle_it	2.839
r_scbond_it	1.78
r_angle_refined_deg	1.354
r_mcangle_it	1.081
r_mcbond_it	0.635
r_nbtor_refined	0.301
r_symmetry_vdw_refined	0.241
r_nbd_refined	0.204
r_xyhbond_nbd_refined	0.162
r_symmetry_hbond_refined	0.123
r_chiral_restr	0.085
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5308
Nucleic Acid Atoms
Solvent Atoms	165
Heterogen Atoms	12

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling
MOLREP	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.