Experiment: 3CQN

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3CQR	AtVDE at pH5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	298	PEG3350, MgNO3, Benzamidine HCl, pH 7, vapor diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.36	43.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.634	α = 82.52
b = 52.458	β = 75.99
c = 54.605	γ = 74.54

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 315		2006-03-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.97625	ESRF	ID23-1

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	2	30	96.9	0.088	0.088	6.2	2	23574	23574	1	1	20.7

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	2	2.11	97.1		0.344	0.344	1.6	2	6787

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	AtVDE at pH5	2	30	22270	22270	1199	96.87	0.2	0.2	0.196	0.272	RANDOM	34.02

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]
-0.23	-0.02	-0.11	0.09	0.02	0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.227
r_dihedral_angle_4_deg	22.792
r_dihedral_angle_3_deg	19.421
r_dihedral_angle_1_deg	9.226
r_scangle_it	4.838
r_scbond_it	3.344
r_angle_refined_deg	2.205
r_mcangle_it	2.189
r_mcbond_it	1.389
r_nbtor_refined	0.326

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.227
r_dihedral_angle_4_deg	22.792
r_dihedral_angle_3_deg	19.421
r_dihedral_angle_1_deg	9.226
r_scangle_it	4.838
r_scbond_it	3.344
r_angle_refined_deg	2.205
r_mcangle_it	2.189
r_mcbond_it	1.389
r_nbtor_refined	0.326
r_nbd_refined	0.257
r_symmetry_vdw_refined	0.257
r_symmetry_hbond_refined	0.215
r_xyhbond_nbd_refined	0.212
r_chiral_restr	0.191
r_bond_refined_d	0.022
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2603
Nucleic Acid Atoms
Solvent Atoms	158
Heterogen Atoms

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection

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 R01GM133198.