Experiment: 3CGM

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1D6O	PDB ENTRY 1D6O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	286	60mg/ml protein, 1:1 mixing, 2M Ammonium sulfate, 2% PEG 400, 1% Thiocyanate, 100mM HEPES, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 286K

Crystal Properties
Matthews coefficient	Solvent content
4.69	73.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.78	α = 90
b = 121.78	β = 90
c = 76.26	γ = 120

Symmetry
Space Group	P 63 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	180	CCD	MARMOSAIC 225 mm CCD	mirrors	2007-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91840	BESSY	14.1

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	2.41	30	96.6	0.093	0.107	21.98	13.1	13374	12921		-3	43.405

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.41	2.55	92.9		0.582	0.45	4.4	11.32	1885

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	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	MR	THROUGHOUT	PDB ENTRY 1D6O	2.41	28.27	-3	13374	11955	969	96.6	0.19	0.187	0.19	0.226	0.2	RANDOM	44.556

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]
-0.13	-0.06		-0.13		0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.398
r_dihedral_angle_4_deg	17.68
r_dihedral_angle_3_deg	16.948
r_dihedral_angle_1_deg	5.994
r_scangle_it	2.189
r_mcangle_it	2.187
r_angle_refined_deg	1.62
r_scbond_it	1.409
r_mcbond_it	1.253
r_chiral_restr	0.093

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1217
Nucleic Acid Atoms
Solvent Atoms	98
Heterogen Atoms	31

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
XDS	data reduction
PHASER	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.