Experiment: 4U8D

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	PEG 8000 10%, Mg(OAc)2 0.2M, cacodylate 0.1M pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
3.48	64.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.832	α = 90
b = 117.832	β = 90
c = 86.88	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	PIXEL	DECTRIS PILATUS 2M		2013-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	1.0000	ELETTRA	5.2R

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim 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	2.3	48.76	99.9	0.099	0.029	0.999	24	12.8		27800			36.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.38	98.9		0.938	0.278	0.88	2.9	12.1	2652

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	PDB ENTRY 4UPG	2.3	48.76	27703	1390	99.65	0.1998	0.1973	0.21	0.2486	0.25	RANDOM	43.793

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]
-1.5			-1.5		3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.496
r_dihedral_angle_4_deg	19.104
r_dihedral_angle_3_deg	16.438
r_dihedral_angle_1_deg	5.314
r_mcangle_it	4.677
r_mcbond_it	2.978
r_mcbond_other	2.975
r_angle_refined_deg	1.458
r_angle_other_deg	0.847
r_chiral_restr	0.087

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.496
r_dihedral_angle_4_deg	19.104
r_dihedral_angle_3_deg	16.438
r_dihedral_angle_1_deg	5.314
r_mcangle_it	4.677
r_mcbond_it	2.978
r_mcbond_other	2.975
r_angle_refined_deg	1.458
r_angle_other_deg	0.847
r_chiral_restr	0.087
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2704
Nucleic Acid Atoms
Solvent Atoms	166
Heterogen Atoms	7

Software

Software
Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
REFMAC	refinement
MOLREP	phasing
XSCALE	data scaling
XSCALE	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.