Experiment: 2O16

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	294	100mM Tris pH 8.5, 2M ammonium phosphate, VAPOR DIFFUSION, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.677	α = 90
b = 58.006	β = 108.85
c = 53.561	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	77	IMAGE PLATE	RIGAKU RAXIS IV	Osmic mirrors	2006-08-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418

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	1.9	20	98.3	0.073	0.073	23.8	7.8	22818	22430

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	1.9	1.97	84.8		0.481	0.481	2.8	5.4	1913

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1XKF	1.9	20	22816	22408	722	98.21	0.176	0.174	0.234	RANDOM	26.349

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]
-0.59		0.61	0.26		0.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.633
r_dihedral_angle_4_deg	14.106
r_dihedral_angle_3_deg	12.293
r_dihedral_angle_1_deg	5.06
r_scangle_it	4.119
r_scbond_it	2.663
r_mcangle_it	1.771
r_angle_refined_deg	1.36
r_mcbond_it	1.189
r_nbtor_refined	0.301

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.633
r_dihedral_angle_4_deg	14.106
r_dihedral_angle_3_deg	12.293
r_dihedral_angle_1_deg	5.06
r_scangle_it	4.119
r_scbond_it	2.663
r_mcangle_it	1.771
r_angle_refined_deg	1.36
r_mcbond_it	1.189
r_nbtor_refined	0.301
r_symmetry_hbond_refined	0.259
r_nbd_refined	0.212
r_symmetry_vdw_refined	0.196
r_xyhbond_nbd_refined	0.171
r_chiral_restr	0.092
r_bond_refined_d	0.015
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2078
Nucleic Acid Atoms
Solvent Atoms	225
Heterogen Atoms	35

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
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 R01GM133198.