Experiment: 3IB7

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	Bis-Tris, amm. acetate, MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.178	α = 90
b = 100.178	β = 90
c = 80.248	γ = 90

Symmetry
Space Group	P 41 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	MAR CCD 165 mm	mirrors	2006-11-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7A	1.008	EMBL/DESY, HAMBURG	BW7A

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	1.6	50	99.9	0.057	11.6	9.4		54354	3	3	26.6

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	1.6	1.64	99.6		0.528	2.3	5	3547

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	PDB ENTRY 2HY1	1.6	32.4	64774	54293	5463	99.85	0.218	0.161	0.159	0.177	RANDOM	25.518

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]
-0.76			-0.76		1.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.926
r_dihedral_angle_3_deg	10.942
r_dihedral_angle_4_deg	10.823
r_dihedral_angle_1_deg	5.413
r_scangle_it	2.012
r_scbond_it	1.226
r_angle_refined_deg	1.162
r_mcangle_it	0.629
r_mcbond_it	0.382
r_nbtor_refined	0.298

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.926
r_dihedral_angle_3_deg	10.942
r_dihedral_angle_4_deg	10.823
r_dihedral_angle_1_deg	5.413
r_scangle_it	2.012
r_scbond_it	1.226
r_angle_refined_deg	1.162
r_mcangle_it	0.629
r_mcbond_it	0.382
r_nbtor_refined	0.298
r_nbd_refined	0.193
r_symmetry_vdw_refined	0.128
r_xyhbond_nbd_refined	0.096
r_symmetry_hbond_refined	0.082
r_chiral_restr	0.078
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2229
Nucleic Acid Atoms
Solvent Atoms	292
Heterogen Atoms	40

Software

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.