Experiment: 1PKV

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1I8D	PDB entry 1I8D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	295	70 mM sodium potassium phosphate, pH 7.0, 100 mM sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.161	α = 90
b = 104.383	β = 90
c = 85.113	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	110	IMAGE PLATE	MARRESEARCH		2000-03-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.8424	EMBL/DESY, HAMBURG	X11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.6	20	99.4			7171	7131

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.63	100

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1I8D	2.6	19.7	7131	6793	337	99.46	0.17699	0.17699	0.17409	0.23469	RANDOM	38.393

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]
-1.58			2.17		-0.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.087
r_scangle_it	5.286
r_scbond_it	3.216
r_mcangle_it	2.151
r_angle_refined_deg	1.798
r_mcbond_it	1.068
r_symmetry_vdw_refined	0.318
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.183
r_chiral_restr	0.112

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.087
r_scangle_it	5.286
r_scbond_it	3.216
r_mcangle_it	2.151
r_angle_refined_deg	1.798
r_mcbond_it	1.068
r_symmetry_vdw_refined	0.318
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.183
r_chiral_restr	0.112
r_bond_refined_d	0.02
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1330
Nucleic Acid Atoms
Solvent Atoms	37
Heterogen Atoms	54

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	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.