Experiment: 3HKD

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1SA0	PDB ENTRY 1SA0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	PEG, PIPES BUFFER, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.91	68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 328.53	α = 90
b = 328.53	β = 90
c = 54.41	γ = 120

Symmetry
Space Group	P 65

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		2006-02-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.978	ESRF	ID14-4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.7	50	98.3	0.074	15.1	8		36232

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	3.7	3.79	97.9		0.605	3.16	7.7

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 1SA0	3.7	20	34182	1839	98.84	0.21194	0.20921	0.26428	RANDOM	42.974

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]
-4.51	-2.26		-4.51		6.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	8.885
r_angle_refined_deg	1.77
r_scangle_it	1.226
r_scbond_it	0.76
r_mcangle_it	0.444
r_symmetry_vdw_refined	0.346
r_nbd_refined	0.286
r_xyhbond_nbd_refined	0.237
r_mcbond_it	0.227
r_metal_ion_refined	0.223

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	8.885
r_angle_refined_deg	1.77
r_scangle_it	1.226
r_scbond_it	0.76
r_mcangle_it	0.444
r_symmetry_vdw_refined	0.346
r_nbd_refined	0.286
r_xyhbond_nbd_refined	0.237
r_mcbond_it	0.227
r_metal_ion_refined	0.223
r_symmetry_hbond_refined	0.147
r_chiral_restr	0.123
r_bond_refined_d	0.017
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14054
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	169

Software

Software
Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

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.