Experiment: 3M0D

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3M0A	PDB entry 3M0A (TRAF2:ciap2)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	277	0.15M AmSO4, 0.1M MES, 15% PEG 4000, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3	58.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.867	α = 90
b = 91.867	β = 90
c = 88.702	γ = 90

Symmetry
Space Group	I 41

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	ADSC QUANTUM 315		2009-08-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A		NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.8	50	99.8	0.097	0.062	8.9	6.1		9137	1	2

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)
1	2.8	2.9	97.8		0.478		4.4	899

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	PDB entry 3M0A (TRAF2:ciap2)	2.8	32.5	8753	436	95.54	0.204	0.197	0.247	RANDOM	52.197

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]
-1.83			-1.83		3.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.749
r_dihedral_angle_3_deg	22.977
r_dihedral_angle_4_deg	16.446
r_dihedral_angle_1_deg	6.294
r_scangle_it	4.461
r_scbond_it	2.517
r_angle_refined_deg	1.622
r_mcangle_it	1.288
r_mcbond_it	0.64
r_chiral_restr	0.121

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.749
r_dihedral_angle_3_deg	22.977
r_dihedral_angle_4_deg	16.446
r_dihedral_angle_1_deg	6.294
r_scangle_it	4.461
r_scbond_it	2.517
r_angle_refined_deg	1.622
r_mcangle_it	1.288
r_mcbond_it	0.64
r_chiral_restr	0.121
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2046
Nucleic Acid Atoms
Solvent Atoms	42
Heterogen Atoms	1

Software

Software
Software Name	Purpose
ADSC	data collection
MOLREP	phasing
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement

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.