Experiment: 3GIM

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	100 mM HEPES, 100 mM Calcium acetate, 10% PEG 4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.668	α = 90
b = 111.924	β = 90
c = 53.158	γ = 90

Symmetry
Space Group	P 21 21 2

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	6144 x 6144 pixel elements with an effective pixel size less than 60x60 micron and resolution of order 90x90 micron	2005-11-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97911	APS	23-ID-D

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	2.7	20	93.8	0.093	18.58	6.1		15930

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	2.7	2.8	72.7		0.493	3	5.1	1198

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 3GIK	2.7	20	15879	797	94.02	0.217	0.214	0.277	RANDOM	56.274

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]
8.92			-5.51		-3.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.247
r_dihedral_angle_3_deg	18.949
r_dihedral_angle_4_deg	16.441
r_dihedral_angle_1_deg	5.212
r_scangle_it	1.632
r_angle_refined_deg	1.522
r_scbond_it	0.917
r_mcangle_it	0.698
r_mcbond_it	0.431
r_metal_ion_refined	0.347

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.247
r_dihedral_angle_3_deg	18.949
r_dihedral_angle_4_deg	16.441
r_dihedral_angle_1_deg	5.212
r_scangle_it	1.632
r_angle_refined_deg	1.522
r_scbond_it	0.917
r_mcangle_it	0.698
r_mcbond_it	0.431
r_metal_ion_refined	0.347
r_nbtor_refined	0.338
r_nbd_refined	0.265
r_symmetry_vdw_refined	0.259
r_symmetry_hbond_refined	0.255
r_xyhbond_nbd_refined	0.223
r_chiral_restr	0.114
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2740
Nucleic Acid Atoms	630
Solvent Atoms	41
Heterogen Atoms	34

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
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.