Experiment: 3PK0

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2UVD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	290	Internal tracking number 216858D10. JCSG+ screen condition D10: 0.2 M CaOAc2, 0.1 M MES cacodylate pH 6.5, 40% PEG300, MysmA.01365.d.A1 PW 28823 at 28.7 mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.56	52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.14	α = 90
b = 78.01	β = 102.22
c = 155.43	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	RIGAKU SATURN 944+		2010-10-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.541780

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	1.75	41.23	96.1	0.057	20.47	7.53	106123	102002		-3	24.209

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	1.75	1.8	85.2		0.48	3.2	4.57	7786

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 (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	2UVD	1.75	41.23	106123	101895	5101	96.03	0.152	0.152	0.15	0.16	0.183	0.19	RANDOM	18.491

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]
-0.03		-0.08	0.27		-0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.896
r_dihedral_angle_4_deg	18.681
r_dihedral_angle_3_deg	11.905
r_dihedral_angle_1_deg	5.518
r_scangle_it	4.273
r_scbond_it	2.543
r_angle_refined_deg	1.52
r_mcangle_it	1.483
r_angle_other_deg	0.997
r_mcbond_it	0.882

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.896
r_dihedral_angle_4_deg	18.681
r_dihedral_angle_3_deg	11.905
r_dihedral_angle_1_deg	5.518
r_scangle_it	4.273
r_scbond_it	2.543
r_angle_refined_deg	1.52
r_mcangle_it	1.483
r_angle_other_deg	0.997
r_mcbond_it	0.882
r_mcbond_other	0.283
r_chiral_restr	0.097
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7293
Nucleic Acid Atoms
Solvent Atoms	878
Heterogen Atoms	59

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	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.