Experiment: 2IDX

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	20% PEG 3350, 0.2 M MgSO4, 10% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.17	61.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.238	α = 90
b = 111.238	β = 90
c = 115.526	γ = 120

Symmetry
Space Group	P 31 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	100	CCD			2005-08-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X26C	1.0	NSLS	X26C

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	2.5	50	100	0.136	9			29063		-2	46.2

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)
	2.5	2.59	100		0.56	2		2884

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1RTY	2.5	30	28765	1428	99	0.2	0.197	0.19	0.251	0.25	RANDOM	34.397

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]
0.56	0.28		0.56		-0.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.842
r_dihedral_angle_4_deg	23.445
r_dihedral_angle_3_deg	18.251
r_dihedral_angle_1_deg	6.068
r_scangle_it	2.88
r_scbond_it	1.849
r_angle_refined_deg	1.484
r_mcangle_it	1.342
r_mcbond_it	0.786
r_nbtor_refined	0.312

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.842
r_dihedral_angle_4_deg	23.445
r_dihedral_angle_3_deg	18.251
r_dihedral_angle_1_deg	6.068
r_scangle_it	2.88
r_scbond_it	1.849
r_angle_refined_deg	1.484
r_mcangle_it	1.342
r_mcbond_it	0.786
r_nbtor_refined	0.312
r_symmetry_hbond_refined	0.241
r_nbd_refined	0.223
r_xyhbond_nbd_refined	0.163
r_symmetry_vdw_refined	0.162
r_metal_ion_refined	0.102
r_chiral_restr	0.095
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3990
Nucleic Acid Atoms
Solvent Atoms	171
Heterogen Atoms	82

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.