Experiment: 3G5D

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	10% PEG 20000, 15% glycerol, 85 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3	59.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.19	α = 78.71
b = 63.69	β = 89.96
c = 74.58	γ = 90.28

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	90	CCD	MARRESEARCH	Dynamically bendable mirror	2008-10-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.99990	SLS	X10SA

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	2.2	40	96.9	0.054	18.75	3.7	38645	37432		-3	34.39

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	2.2	2.3	96.6		0.145	9.7	3.69	4637

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 2OIQ	2.2	35.05	38645	37431	936	100	0.207	0.206	0.257	RANDOM	30.597

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]
0.15	-0.01	-0.12	0.85	-0.16	-0.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.594
r_dihedral_angle_4_deg	17.338
r_dihedral_angle_3_deg	16.218
r_dihedral_angle_1_deg	6.115
r_scangle_it	3.319
r_scbond_it	2.157
r_angle_refined_deg	1.549
r_mcangle_it	1.453
r_mcbond_it	0.882
r_nbtor_refined	0.307

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.594
r_dihedral_angle_4_deg	17.338
r_dihedral_angle_3_deg	16.218
r_dihedral_angle_1_deg	6.115
r_scangle_it	3.319
r_scbond_it	2.157
r_angle_refined_deg	1.549
r_mcangle_it	1.453
r_mcbond_it	0.882
r_nbtor_refined	0.307
r_symmetry_vdw_refined	0.217
r_symmetry_hbond_refined	0.215
r_nbd_refined	0.207
r_xyhbond_nbd_refined	0.169
r_chiral_restr	0.094
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4138
Nucleic Acid Atoms
Solvent Atoms	225
Heterogen Atoms	78

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data scaling

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.