Experiment: 3OJ4

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1UBQ	PDB ENTRY: 1UBQ, 1X23
experimental model	PDB	1X23	PDB ENTRY: 1UBQ, 1X23

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.1	292	0.1 M HEPES pH 7.1 and 1.85 M Na Malonate pH 7.0, VAPOR DIFFUSION, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.646	α = 90
b = 102.646	β = 90
c = 112.686	γ = 120

Symmetry
Space Group	P 3 2 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	ADSC QUANTUM 210		2006-10-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	1.0000	ALS	5.0.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.4	25	98.2	0.115	16.8	6.1	9814	9637		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	3.4	3.52	99.8		0.75	3.3	3.9	955

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY: 1UBQ, 1X23	3.4	25	9612	8650	962	98.09	0.284	0.28381	0.27984	0.31882	RANDOM	94.095

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]
-3.19	-1.6		-3.19		4.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.848
r_dihedral_angle_3_deg	18.909
r_dihedral_angle_4_deg	12.395
r_dihedral_angle_1_deg	5.313
r_scangle_it	1.823
r_mcangle_it	1.281
r_scbond_it	1.253
r_angle_refined_deg	1.013
r_mcbond_it	0.834
r_symmetry_vdw_refined	0.323

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.848
r_dihedral_angle_3_deg	18.909
r_dihedral_angle_4_deg	12.395
r_dihedral_angle_1_deg	5.313
r_scangle_it	1.823
r_mcangle_it	1.281
r_scbond_it	1.253
r_angle_refined_deg	1.013
r_mcbond_it	0.834
r_symmetry_vdw_refined	0.323
r_nbtor_refined	0.302
r_symmetry_hbond_refined	0.208
r_nbd_refined	0.194
r_xyhbond_nbd_refined	0.125
r_chiral_restr	0.07
r_bond_refined_d	0.009
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3986
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	2

Software

Software
Software Name	Purpose
BOS	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	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.