Experiment: 6EDF

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3UF4	PDB entry 3UF4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	20% PEG3350, 0.2 M magnesium acetate

Crystal Properties
Matthews coefficient	Solvent content
2	37.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 23.991	α = 90
b = 36.233	β = 99.52
c = 38.646	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	RAYONIX MX-300		2010-05-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.9795	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.4	36.23	98.4	0.053	0.063	0.032	0.999	16.5	3.7		12781

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.42	87.7		0.4	0.487	0.272	0.817		3.1	564

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3UF4	1.4	26.27	12154	619	98.24	0.1448	0.1434	0.16	0.1721	0.18	12.097

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]
-0.6		-0.38	-0.26		0.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_4_deg	27.296
r_dihedral_angle_2_deg	23.291
r_dihedral_angle_3_deg	10.424
r_dihedral_angle_1_deg	6.004
r_mcangle_it	2.79
r_mcbond_it	1.914
r_angle_refined_deg	1.848
r_mcbond_other	1.809
r_angle_other_deg	1.102
r_chiral_restr	0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_4_deg	27.296
r_dihedral_angle_2_deg	23.291
r_dihedral_angle_3_deg	10.424
r_dihedral_angle_1_deg	6.004
r_mcangle_it	2.79
r_mcbond_it	1.914
r_angle_refined_deg	1.848
r_mcbond_other	1.809
r_angle_other_deg	1.102
r_chiral_restr	0.1
r_bond_refined_d	0.016
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	587
Nucleic Acid Atoms
Solvent Atoms	61
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
PDB_EXTRACT	data extraction

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.