Experiment: 2PN5

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	294	2 M NaH2/K2H PO4, 0.2 M NaCl, 0.1 M imidazole pH 8.0, 50 mM NaK tartrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
4.26	71.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 150.515	α = 90
b = 150.515	β = 90
c = 226.315	γ = 90

Symmetry
Space Group	P 43 21 2

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	APS-1	SAGITALLY FOCUSING. 2ND CRYSTAL, ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR	2006-11-11	M	SINGLE WAVELENGTH
2	1
3	1
4	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.9791	APS	19-BM

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	2.698	50	99.9	0.08	10.1	7.8	72031	71959	-1	-1	69.24

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	2.698	2.75	99.9		0.898	2.1	7.5	3537

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MIRAS	THROUGHOUT	2.698	45.88	71859	71859	3631	100	0.239	0.275	RANDOM	52.085

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]
1.23			1.23		-2.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.85
r_dihedral_angle_4_deg	19.75
r_dihedral_angle_3_deg	18.161
r_dihedral_angle_1_deg	5.962
r_scangle_it	2.159
r_scbond_it	1.217
r_angle_refined_deg	1.188
r_mcangle_it	0.958
r_mcbond_it	0.503
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.85
r_dihedral_angle_4_deg	19.75
r_dihedral_angle_3_deg	18.161
r_dihedral_angle_1_deg	5.962
r_scangle_it	2.159
r_scbond_it	1.217
r_angle_refined_deg	1.188
r_mcangle_it	0.958
r_mcbond_it	0.503
r_nbtor_refined	0.309
r_nbd_refined	0.209
r_symmetry_vdw_refined	0.191
r_symmetry_hbond_refined	0.142
r_xyhbond_nbd_refined	0.125
r_chiral_restr	0.083
r_bond_refined_d	0.009
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10270
Nucleic Acid Atoms
Solvent Atoms	140
Heterogen Atoms	73

Software

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.