Experiment: 3FDO

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DAB	PDB ENTRY 3DAB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.3	290	4.3M NaCl, 100mM Hepes, pH7.3, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
1.89	35.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.23	α = 90
b = 30.95	β = 124.41
c = 50.42	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	90	CCD	MARRESEARCH	monochromator	2008-07-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.0	SLS	X10SA

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	1.4	30	84.1			17646	14843	2	2

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	1.4	1.5	46.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	THROUGHOUT	PDB ENTRY 3DAB	1.4	15	2	17646	13765	768	84.53	0.1881	0.18286	0.17936	0.17	0.24708	0.24	RANDOM	19.143

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]
-0.91		-0.29	1.37		-0.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.049
r_dihedral_angle_4_deg	21.448
r_dihedral_angle_3_deg	13.869
r_dihedral_angle_1_deg	13.028
r_scangle_it	3.493
r_sphericity_free	3.27
r_sphericity_bonded	2.823
r_scbond_it	2.292
r_mcangle_it	1.552
r_rigid_bond_restr	1.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.049
r_dihedral_angle_4_deg	21.448
r_dihedral_angle_3_deg	13.869
r_dihedral_angle_1_deg	13.028
r_scangle_it	3.493
r_sphericity_free	3.27
r_sphericity_bonded	2.823
r_scbond_it	2.292
r_mcangle_it	1.552
r_rigid_bond_restr	1.31
r_angle_refined_deg	1.304
r_mcbond_it	0.916
r_chiral_restr	0.11
r_bond_refined_d	0.008
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	818
Nucleic Acid Atoms
Solvent Atoms	165
Heterogen Atoms	5

Software

Software
Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

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.