4KMF | pdb_00004kmf

Crystal structure of Zalpha domain from Carassius auratus PKZ in complex with Z-DNA

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		295	30% PEG1500, 15 mM MnCl2, vapor diffusion, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.367	α = 90
b = 49.471	β = 97.22
c = 29.585	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 210		2006-10-23		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 4A	1.0	PAL/PLS	4A

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	1.7	50	97.5	0.061	15.4	3.4		8549

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	1.7	1.73	89.9		0.325		3	399

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.7	27.46	8535	404	97.32	0.1729	0.1704	0.17	0.2269	0.22	RANDOM	24.5162

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]
-0.01		0.01	0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.838
r_dihedral_angle_4_deg	18.651
r_dihedral_angle_3_deg	15.305
r_dihedral_angle_1_deg	5.686
r_scangle_it	5.25
r_scbond_it	3.734
r_mcangle_it	2.244
r_rigid_bond_restr	2.044
r_angle_refined_deg	1.602
r_mcbond_it	1.281

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.838
r_dihedral_angle_4_deg	18.651
r_dihedral_angle_3_deg	15.305
r_dihedral_angle_1_deg	5.686
r_scangle_it	5.25
r_scbond_it	3.734
r_mcangle_it	2.244
r_rigid_bond_restr	2.044
r_angle_refined_deg	1.602
r_mcbond_it	1.281
r_chiral_restr	0.1
r_bond_refined_d	0.014
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	490
Nucleic Acid Atoms	139
Solvent Atoms	70
Heterogen Atoms	1

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	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.