Experiment: 5D10

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.085-0.125 mM MES, 9-11.5 % PEG20000

Crystal Properties
Matthews coefficient	Solvent content
3.05	59.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.9	α = 79.2
b = 63.5	β = 88.1
c = 76.6	γ = 90.1

Symmetry
Space Group	P 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	IMAGE PLATE	MAR scanner 345 mm plate		2011-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5417

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	2.7	45	87.9	0.066	0.086	12.17	2.39		18728		-3	28.017

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.8	94		0.183	0.238	5.73

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2OIQ	2.7	44.11	17978	750	87.9	0.2724	0.269	0.3592	RANDOM	28.792

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]
-0.94	0.72	0.04	-0.93	0.03	1.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.37
r_dihedral_angle_3_deg	19.51
r_dihedral_angle_4_deg	17.925
r_dihedral_angle_1_deg	8.877
r_mcangle_it	2.782
r_angle_refined_deg	1.892
r_mcbond_it	1.632
r_mcbond_other	1.632
r_angle_other_deg	1.187
r_chiral_restr	0.097

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.37
r_dihedral_angle_3_deg	19.51
r_dihedral_angle_4_deg	17.925
r_dihedral_angle_1_deg	8.877
r_mcangle_it	2.782
r_angle_refined_deg	1.892
r_mcbond_it	1.632
r_mcbond_other	1.632
r_angle_other_deg	1.187
r_chiral_restr	0.097
r_bond_refined_d	0.014
r_bond_other_d	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3946
Nucleic Acid Atoms
Solvent Atoms	100
Heterogen Atoms	64

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
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 R01GM157729.