Experiment: 6XOI

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Y8R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	50 mM BisTris, pH 6.5, 50 mM Ammonium Sulfate, 30% pentaerythritol ethoxylate (Hampton Index 57)

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.224	α = 90
b = 72.4	β = 93.293
c = 127.407	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	100	CCD	RAYONIX MX225HE		2011-03-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.9793	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	19.38	95.62	0.07504	0.996	12.96	3.7		69609

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.071			0.7795	0.66	1.7

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1Y8R	2	19.38	68529	6927	95.641	0.244	0.2388	0.2873	40.672

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]
-0.062		0.205	-0.109		0.147

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.205
r_dihedral_angle_4_deg	19.134
r_dihedral_angle_3_deg	17.991
r_lrange_it	7.452
r_dihedral_angle_1_deg	6.584
r_scangle_it	5.452
r_mcangle_it	4.581
r_scbond_it	3.937
r_mcbond_it	3.265
r_angle_refined_deg	1.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.205
r_dihedral_angle_4_deg	19.134
r_dihedral_angle_3_deg	17.991
r_lrange_it	7.452
r_dihedral_angle_1_deg	6.584
r_scangle_it	5.452
r_mcangle_it	4.581
r_scbond_it	3.937
r_mcbond_it	3.265
r_angle_refined_deg	1.5
r_nbtor_refined	0.31
r_symmetry_nbd_refined	0.23
r_nbd_refined	0.229
r_symmetry_xyhbond_nbd_refined	0.164
r_xyhbond_nbd_refined	0.149
r_chiral_restr	0.112
r_gen_planes_refined	0.008
r_bond_refined_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5839
Nucleic Acid Atoms
Solvent Atoms	286
Heterogen Atoms	40

Software

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