Experiment: 3KO9

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		PfDTD-Iodide model (not deposited)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	25% PEG 1500, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.252	α = 106.94
b = 54.863	β = 101.63
c = 92.419	γ = 94.49

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	IMAGE PLATE	MAR scanner 345 mm plate		2008-10-13		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

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	2.75	30	97.3	0.053	14.1	3.9		24028

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)
	2.75	2.85	94.3		0.521		3.6	2303

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	PfDTD-Iodide model (not deposited)	2.75	30	24027	1218	97.35	0.205	0.201	0.275	RANDOM	74.366

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]
0.02	-0.74	2.46	2.08	3.77	0.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	45.666
r_dihedral_angle_4_deg	23.115
r_dihedral_angle_3_deg	19.053
r_dihedral_angle_1_deg	6.56
r_scangle_it	1.714
r_angle_refined_deg	1.282
r_mcangle_it	1.056
r_scbond_it	1.037
r_mcbond_it	0.587
r_nbtor_refined	0.314

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	45.666
r_dihedral_angle_4_deg	23.115
r_dihedral_angle_3_deg	19.053
r_dihedral_angle_1_deg	6.56
r_scangle_it	1.714
r_angle_refined_deg	1.282
r_mcangle_it	1.056
r_scbond_it	1.037
r_mcbond_it	0.587
r_nbtor_refined	0.314
r_nbd_refined	0.218
r_symmetry_vdw_refined	0.207
r_symmetry_hbond_refined	0.17
r_xyhbond_nbd_refined	0.159
r_chiral_restr	0.085
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7357
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	12

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	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.