Experiment: 2PFY

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	277	3.8M Potassium Acetate, 0.1M Sodium Citrate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.11	60.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.84	α = 90
b = 149.75	β = 90
c = 169.58	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	ADSC QUANTUM 315		2006-03-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.97935	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.95	112.51					111077

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.95	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.95	112.51	111007	5579	91.75	0.169	0.168	0.201	RANDOM	35.864

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]
0.07			-0.04		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.023
r_dihedral_angle_4_deg	21.4
r_dihedral_angle_3_deg	16.295
r_dihedral_angle_1_deg	6.023
r_angle_refined_deg	1.465
r_angle_other_deg	0.59
r_nbtor_refined	0.3
r_nbtor_other	0.278
r_nbd_refined	0.224
r_xyhbond_nbd_refined	0.206

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.023
r_dihedral_angle_4_deg	21.4
r_dihedral_angle_3_deg	16.295
r_dihedral_angle_1_deg	6.023
r_angle_refined_deg	1.465
r_angle_other_deg	0.59
r_nbtor_refined	0.3
r_nbtor_other	0.278
r_nbd_refined	0.224
r_xyhbond_nbd_refined	0.206
r_nbd_other	0.198
r_chiral_restr	0.104
r_bond_refined_d	0.016
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_symmetry_vdw_refined

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9232
Nucleic Acid Atoms
Solvent Atoms	754
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
XDS	data reduction
XSCALE	data scaling
SHARP	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.