Experiment: 3DQ0

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BW7	PDB ENTRY 3BW7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	15% PEG 1500, 0.5% n-octyl beta-D-glucoside, Tris-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.93	57.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 252.7	α = 90
b = 50.4	β = 93.7
c = 51	γ = 90

Symmetry
Space Group	C 1 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 315		2007-03-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.98	ESRF	BM30A

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	1.9	46.18	94.7	0.043	17.95			48203		-3	27.988

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	1.9	2	87.9		0.159	7		6334

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	PDB ENTRY 3BW7	1.9	46.18	48202	4821	94.7	0.207	0.204	0.237	RANDOM	25.086

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]
-1.45		-0.04	2.09		-0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.136
r_dihedral_angle_4_deg	17.535
r_dihedral_angle_3_deg	13.462
r_dihedral_angle_1_deg	5.541
r_scangle_it	1.831
r_scbond_it	1.123
r_angle_refined_deg	1.099
r_mcangle_it	0.872
r_mcbond_it	0.499
r_nbtor_refined	0.303

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.136
r_dihedral_angle_4_deg	17.535
r_dihedral_angle_3_deg	13.462
r_dihedral_angle_1_deg	5.541
r_scangle_it	1.831
r_scbond_it	1.123
r_angle_refined_deg	1.099
r_mcangle_it	0.872
r_mcbond_it	0.499
r_nbtor_refined	0.303
r_nbd_refined	0.185
r_symmetry_vdw_refined	0.178
r_symmetry_hbond_refined	0.155
r_xyhbond_nbd_refined	0.123
r_chiral_restr	0.074
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3800
Nucleic Acid Atoms
Solvent Atoms	365
Heterogen Atoms	169

Software

Software
Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.