Experiment: 2PKD

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	294	20% PEG3350, 0.3 M MgCl2, 0.1 M, HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.013	α = 90
b = 170.982	β = 90
c = 148.527	γ = 90

Symmetry
Space Group	C 2 2 21

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	MAR CCD 165 mm	X9A	2005-09-26	M	MAD
2	1	x-ray	100	CCD	ADSC QUANTUM 315	X29A	2005-09-26	M	SINGLE WAVELENGTH
3	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X9A	0.961, 0.9797, 0.9794	NSLS	X9A
2	SYNCHROTRON	NSLS BEAMLINE X29A	1.1	NSLS	X29A

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	1.98	50	90.2	0.072	11.3	3.6		39739

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)
	1.98	2.05	15.1		0.406		1.3	810

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.043	20	39654	1999	79.98	0.201	0.197	0.277	RANDOM	44.174

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]
-0.06			-0.02		0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.466
r_dihedral_angle_4_deg	21.592
r_dihedral_angle_3_deg	18.91
r_dihedral_angle_1_deg	7.821
r_scangle_it	5.37
r_scbond_it	3.412
r_mcangle_it	2.68
r_angle_refined_deg	1.938
r_mcbond_it	1.56
r_nbtor_refined	0.321

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.466
r_dihedral_angle_4_deg	21.592
r_dihedral_angle_3_deg	18.91
r_dihedral_angle_1_deg	7.821
r_scangle_it	5.37
r_scbond_it	3.412
r_mcangle_it	2.68
r_angle_refined_deg	1.938
r_mcbond_it	1.56
r_nbtor_refined	0.321
r_symmetry_vdw_refined	0.266
r_nbd_refined	0.241
r_symmetry_hbond_refined	0.234
r_xyhbond_nbd_refined	0.18
r_chiral_restr	0.136
r_bond_refined_d	0.023
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5243
Nucleic Acid Atoms
Solvent Atoms	393
Heterogen Atoms	2

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
SHELXS	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 R01GM157729.