Experiment: 5F09

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4NPG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	288.15	33% (v/v) pentaerythritol propoxylate PO/OH 5/4 (Hampton Research, Aliso Viejo, Ca, USA), 1.5% (w/v) PEG 3350 (Merck KGaA, Darmstadt, Germany) and 0.10 M Tris-HCl (Merck KGaA), pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
3.35	63.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.901	α = 90
b = 130.923	β = 90
c = 159.136	γ = 90

Symmetry
Space Group	I 2 2 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	PIXEL	PSI PILATUS 6M		2014-07-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.918	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.85	30	98.8	0.081	0.081	13.29	4.51		89051		-3	35.174

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.96	97.1		0.94	0.941	1.96	4.43

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	4NPG	1.85	30	84513	4444	99.04	0.1565	0.1552	0.1814	RANDOM	40.583

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]
0.58			-1.69		1.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.923
r_dihedral_angle_4_deg	15.467
r_sphericity_free	13.418
r_dihedral_angle_3_deg	12.862
r_sphericity_bonded	9.865
r_dihedral_angle_1_deg	6.176
r_mcangle_it	1.695
r_angle_refined_deg	1.69
r_mcbond_it	1.033
r_mcbond_other	1.033

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.923
r_dihedral_angle_4_deg	15.467
r_sphericity_free	13.418
r_dihedral_angle_3_deg	12.862
r_sphericity_bonded	9.865
r_dihedral_angle_1_deg	6.176
r_mcangle_it	1.695
r_angle_refined_deg	1.69
r_mcbond_it	1.033
r_mcbond_other	1.033
r_angle_other_deg	1.02
r_chiral_restr	0.095
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_gen_planes_other	0.004
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5492
Nucleic Acid Atoms
Solvent Atoms	562
Heterogen Atoms	223

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
XDS	data reduction
Coot	model building

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.