Experiment: 5KXY

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BLX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	291	CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (1.0 M SODIUM CHLORIDE, 50 MM SODIUM ACETATE PH 4.5) AND PROTEIN (40-60 MG/ML)

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.159	α = 90
b = 79.159	β = 90
c = 37.956	γ = 90

Symmetry
Space Group	P 43 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	278	CCD	MARMOSAIC 325 mm CCD		2013-07-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL14-1	1.21549	SSRL	BL14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.198	31.414	93.7	0.123	0.143	0.071	7.3	3.5	35831	35831

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.2	1.26	85.9		2.113	2.113	2.497	1.285	0.3	3	4730

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	FOURIER SYNTHESIS	THROUGHOUT	2BLX	1.2	31.414	32587	1703	89.07	0.1823	0.1809	0.19	0.2103	0.22	RANDOM	17.338

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]
-0.21			-0.21		0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.844
r_dihedral_angle_4_deg	20.07
r_dihedral_angle_3_deg	13.023
r_dihedral_angle_1_deg	6.82
r_mcangle_it	2.464
r_angle_refined_deg	2.267
r_mcbond_it	1.598
r_mcbond_other	1.551
r_angle_other_deg	1.201
r_chiral_restr	0.142

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.844
r_dihedral_angle_4_deg	20.07
r_dihedral_angle_3_deg	13.023
r_dihedral_angle_1_deg	6.82
r_mcangle_it	2.464
r_angle_refined_deg	2.267
r_mcbond_it	1.598
r_mcbond_other	1.551
r_angle_other_deg	1.201
r_chiral_restr	0.142
r_bond_refined_d	0.022
r_gen_planes_refined	0.012
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	53
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
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.