Experiment: 5N48

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4GH7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	29 % (w/v) PEG4000, 0.1 M Na-malonate

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.456	α = 90
b = 67.801	β = 90.06
c = 76.806	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	MARMOSAIC 225 mm CCD		2011-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.91741	BESSY	14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	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	1.6	28.47	99.7	0.057	0.065	0.998	14.85	4.18		70827		-3	25.453

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.7	99.8		0.423	0.485	0.879	3.33	4.172

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	4GH7	1.6	28.47	67277	3545	99.42	0.1707	0.1688	0.2078	RANDOM	22.795

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]
-10.75		1.05	27.05		-16.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.343
r_dihedral_angle_3_deg	16.063
r_dihedral_angle_4_deg	14.642
r_dihedral_angle_1_deg	7.508
r_angle_refined_deg	1.918
r_angle_other_deg	1.136
r_chiral_restr	0.117
r_bond_refined_d	0.019
r_gen_planes_refined	0.011
r_gen_planes_other	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.343
r_dihedral_angle_3_deg	16.063
r_dihedral_angle_4_deg	14.642
r_dihedral_angle_1_deg	7.508
r_angle_refined_deg	1.918
r_angle_other_deg	1.136
r_chiral_restr	0.117
r_bond_refined_d	0.019
r_gen_planes_refined	0.011
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4217
Nucleic Acid Atoms
Solvent Atoms	296
Heterogen Atoms

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	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.