Experiment: 3CD8

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2RFN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.8	298	0.1M HEPES pH 7.8, 15% PEG 4K, 6% 2-Propanol, 40mM BME, and 3% Ethanol, VAPOR DIFFUSION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.008	α = 90
b = 43.208	β = 90
c = 158.219	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	130	IMAGE PLATE	RIGAKU RAXIS IV++	varimax optics	2006-04-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2	50	94.3	0.056	29	3.5	20427	19263	-1	-1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2	2.07	78.8		0.193	6.2	2.3	1587

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2RFN	2	50	19218	18215	973	94.78	0.23587	0.23587	0.23328	0.28678	RANDOM	32.191

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]
-0.74			2.99		-2.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.953
r_dihedral_angle_4_deg	14.852
r_dihedral_angle_3_deg	13.747
r_dihedral_angle_1_deg	5.189
r_scangle_it	1.444
r_angle_refined_deg	1.105
r_scbond_it	0.994
r_mcangle_it	0.907
r_mcbond_it	0.554
r_nbtor_refined	0.301

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.953
r_dihedral_angle_4_deg	14.852
r_dihedral_angle_3_deg	13.747
r_dihedral_angle_1_deg	5.189
r_scangle_it	1.444
r_angle_refined_deg	1.105
r_scbond_it	0.994
r_mcangle_it	0.907
r_mcbond_it	0.554
r_nbtor_refined	0.301
r_nbd_refined	0.176
r_xyhbond_nbd_refined	0.126
r_symmetry_hbond_refined	0.109
r_symmetry_vdw_refined	0.105
r_chiral_restr	0.072
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2189
Nucleic Acid Atoms
Solvent Atoms	140
Heterogen Atoms	29

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	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.