Experiment: 1ZF6

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	100D	ndb entry AHJ060

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	Na Cacodylate, CaCl2, Spermine, MPD in resevoir, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.89	35.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 25.239	α = 90
b = 41.179	β = 90
c = 44.41	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	103	CCD	ADSC QUANTUM 4		2004-02-25		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-D	0.9795	APS	14-BM-D

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	1.45	16	93	0.051	28.5			8116

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)
	1.45	1.5	51.9	51.9	0.289	0.289	2.71

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 (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	ndb entry AHJ060	1.5	15.95	6829	815	100	0.262	0.256	0.306	RANDOM	5.034

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]
-0.1			0.26		-0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_angle_refined_deg	2.786
r_scangle_it	1.449
r_scbond_it	1.151
r_nbtor_refined	0.322
r_nbd_refined	0.25
r_symmetry_vdw_refined	0.247
r_xyhbond_nbd_refined	0.228
r_symmetry_hbond_refined	0.142
SYMMETRY METAL-ION REFINED ATOMS (A)	0.138
r_chiral_restr	0.112

RMS Deviations
Key	Refinement Restraint Deviation
r_angle_refined_deg	2.786
r_scangle_it	1.449
r_scbond_it	1.151
r_nbtor_refined	0.322
r_nbd_refined	0.25
r_symmetry_vdw_refined	0.247
r_xyhbond_nbd_refined	0.228
r_symmetry_hbond_refined	0.142
SYMMETRY METAL-ION REFINED ATOMS (A)	0.138
r_chiral_restr	0.112
POTENTIAL METAL-ION REFINED ATOMS (A)	0.084
r_gen_planes_refined	0.011
r_bond_refined_d	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	404
Solvent Atoms	116
Heterogen Atoms	4

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
EPMR	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 R01GM133198.