Experiment: 2EFW

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1F4K	PDB ENTRY 1F4K (with residues 72 to 88 and the DNA removed)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	295	2% PEG 4000, 125mM sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.97	58.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.012	α = 90
b = 129.626	β = 90
c = 125.221	γ = 90

Symmetry
Space Group	C 2 2 21

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 4		2003-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.90	APS	14-BM-C

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	2.5	50	94.3	0.091	12.7	4.7		32161	1	1	52.4

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	2.5	2.56	84.8		0.341	2.3	2.1

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 1F4K (with residues 72 to 88 and the DNA removed)	2.5	50	32161	1729	96.21	0.29303	0.29095	0.33221	RANDOM	11.106

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]
-4.25			-3.33		7.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.025
r_dihedral_angle_3_deg	21.391
r_dihedral_angle_4_deg	19.929
r_dihedral_angle_1_deg	5.665
r_scangle_it	1.694
r_angle_refined_deg	1.532
r_scbond_it	1.041
r_mcangle_it	0.712
r_mcbond_it	0.408
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.025
r_dihedral_angle_3_deg	21.391
r_dihedral_angle_4_deg	19.929
r_dihedral_angle_1_deg	5.665
r_scangle_it	1.694
r_angle_refined_deg	1.532
r_scbond_it	1.041
r_mcangle_it	0.712
r_mcbond_it	0.408
r_nbtor_refined	0.309
r_symmetry_hbond_refined	0.247
r_nbd_refined	0.245
r_xyhbond_nbd_refined	0.242
r_symmetry_vdw_refined	0.196
r_chiral_restr	0.081
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3787
Nucleic Acid Atoms	1546
Solvent Atoms	24
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

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.