Experiment: 5VC9

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		unpublished model of related protein-DNA complex

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	291	30% PEG-1500, 5% MPD, 0.2 M sodium chloride, 0.1 M HEPES

Crystal Properties
Matthews coefficient	Solvent content
2.4	49.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 29.983	α = 70.98
b = 40.29	β = 86.43
c = 57.76	γ = 67.83

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		2013-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97918	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.1	27.24	97.2	0.061	0.081	0.054	0.995	10.1	2.1		13389

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.16	92.6		0.597	0.82	0.559	0.653		1.8	1057

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X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	unpublished model of related protein-DNA complex	2.1	27.2	12637	750	97.13	0.2132	0.211	0.22	0.2481	0.25	thin resolution shells (sftools)	45.818

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]
2.36	0.7	-0.78	-1.17	0.4	0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.972
r_dihedral_angle_4_deg	23.25
r_dihedral_angle_3_deg	11.367
r_dihedral_angle_1_deg	6.769
r_mcangle_it	2.489
r_mcbond_other	1.783
r_mcbond_it	1.781
r_angle_refined_deg	1.554
r_angle_other_deg	1.474
r_chiral_restr	0.092

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.972
r_dihedral_angle_4_deg	23.25
r_dihedral_angle_3_deg	11.367
r_dihedral_angle_1_deg	6.769
r_mcangle_it	2.489
r_mcbond_other	1.783
r_mcbond_it	1.781
r_angle_refined_deg	1.554
r_angle_other_deg	1.474
r_chiral_restr	0.092
r_bond_refined_d	0.017
r_gen_planes_refined	0.012
r_bond_other_d	0.005
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	668
Nucleic Acid Atoms	972
Solvent Atoms	30
Heterogen Atoms	11

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction

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.