Experiment: 3KO4

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 3350. 0.1 MES , pH 6.2-6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.174	α = 72.86
b = 53.005	β = 76.45
c = 90.432	γ = 88.32

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	CCD	MARMOSAIC 225 mm CCD		2007-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.97	ESRF	BM14

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	2.7	25	81.3	0.08	6.9	2.7		19638

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)
	2.7	2.8	44.9		0.387		2.4	1080

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)	2.7	20	19597	1013	81.12	0.214	0.21	0.285	RANDOM	57.401

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]
3.05	-0.53	-5.23	-4.36	0.04	3.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	44.347
r_dihedral_angle_4_deg	19.455
r_dihedral_angle_3_deg	18.961
r_dihedral_angle_1_deg	6.722
r_scangle_it	1.495
r_angle_refined_deg	1.283
r_mcangle_it	0.951
r_scbond_it	0.914
r_mcbond_it	0.522
r_nbtor_refined	0.316

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	44.347
r_dihedral_angle_4_deg	19.455
r_dihedral_angle_3_deg	18.961
r_dihedral_angle_1_deg	6.722
r_scangle_it	1.495
r_angle_refined_deg	1.283
r_mcangle_it	0.951
r_scbond_it	0.914
r_mcbond_it	0.522
r_nbtor_refined	0.316
r_symmetry_hbond_refined	0.311
r_symmetry_vdw_refined	0.267
r_nbd_refined	0.221
r_xyhbond_nbd_refined	0.163
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	7458
Nucleic Acid Atoms
Solvent Atoms	10
Heterogen Atoms	81

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.