Experiment: 3K2M

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OPK	1OPK: 154-235, 1FNF: loops omitted
experimental model	PDB	1FNF	1OPK: 154-235, 1FNF: loops omitted

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	30% PEG 4000, 0.2M sodium acetate trihydrate, 0.1M Tris hydrochloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.625	α = 90
b = 88.181	β = 90
c = 131.081	γ = 90

Symmetry
Space Group	P 21 21 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	IMAGE PLATE	MAR scanner 345 mm plate		2008-10-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.97872	APS	21-ID-D

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	1.751	50	95.3	0.046		6.1		38402		2

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)
1	1.751	1.81	65		0.438	1.9	2.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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	1OPK: 154-235, 1FNF: loops omitted	1.75	39	2	40297	38402	1922	95.3	0.183	0.182	0.18	0.221	RANDOM	27.667

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]
-0.76			-0.18		0.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.396
r_dihedral_angle_4_deg	19.742
r_dihedral_angle_3_deg	11.706
r_dihedral_angle_1_deg	5.955
r_scangle_it	2.935
r_scbond_it	2.27
r_angle_refined_deg	1.5
r_mcangle_it	1.482
r_mcbond_it	0.934
r_nbtor_refined	0.303

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.396
r_dihedral_angle_4_deg	19.742
r_dihedral_angle_3_deg	11.706
r_dihedral_angle_1_deg	5.955
r_scangle_it	2.935
r_scbond_it	2.27
r_angle_refined_deg	1.5
r_mcangle_it	1.482
r_mcbond_it	0.934
r_nbtor_refined	0.303
r_symmetry_vdw_refined	0.232
r_nbd_refined	0.201
r_symmetry_hbond_refined	0.196
r_xyhbond_nbd_refined	0.147
r_chiral_restr	0.101
r_bond_refined_d	0.017
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3089
Nucleic Acid Atoms
Solvent Atoms	286
Heterogen Atoms	10

Software

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