Experiment: 3NBU

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	298	25% PEG 3350, 0.2M ammonium acetate, 0.1M Bis-Tris 5.5, 10 mM betaine HCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.806	α = 92.47
b = 72.874	β = 97.82
c = 181.851	γ = 114.57

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	CCD	ADSC QUANTUM 315r	KOHZU: Double Crystal Si(111)	2007-10-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.11587	ALS	8.3.1

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	1.99	89	94.6	0.104	0.104	9.7	2	208294	208294	1	1	23

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	1.99	2.1	94.6		0.423	0.423	1.7	2	29607

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1dqr	2.05	89	181581	9609	94.94	0.17227	0.16923	0.1705	0.22952	0.2299	RANDOM	23.059

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]
0.88	-1.16	-0.82	-1.03	-1.09	-1.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.219
r_dihedral_angle_4_deg	15.94
r_dihedral_angle_3_deg	15.144
r_dihedral_angle_1_deg	5.797
r_scangle_it	4.577
r_scbond_it	3.045
r_mcangle_it	1.689
r_angle_refined_deg	1.313
r_mcbond_it	0.985
r_chiral_restr	0.095

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.219
r_dihedral_angle_4_deg	15.94
r_dihedral_angle_3_deg	15.144
r_dihedral_angle_1_deg	5.797
r_scangle_it	4.577
r_scbond_it	3.045
r_mcangle_it	1.689
r_angle_refined_deg	1.313
r_mcbond_it	0.985
r_chiral_restr	0.095
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	25984
Nucleic Acid Atoms
Solvent Atoms	3262
Heterogen Atoms	1

Software

Software
Software Name	Purpose
Blu-Ice	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	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.