Experiment: 5OPK

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5K7Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	0.1 M MES/imidazole pH 6.5; 0.03 M of each divalent cation; 10% w/v PEG 8000, 20% v/v ethylene glycol (Morpheus condition A2)

Crystal Properties
Matthews coefficient	Solvent content
3.43	64.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.579	α = 90
b = 127.104	β = 90
c = 130.317	γ = 90

Symmetry
Space Group	I 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2015-04-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.918409	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	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	1.736	48.99	98.8	0.093	0.101	0.998	13.6	6.5		77607			29.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.74	1.84	94.6		0.83	0.905	0.823	1.88	6.21

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5K7Y	1.74	48.99	73724	3881	98.8	0.1797	0.1785	0.19	0.2034	0.21	RANDOM	29.152

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.927
r_dihedral_angle_4_deg	16.702
r_dihedral_angle_3_deg	13.14
r_dihedral_angle_1_deg	6.133
r_angle_other_deg	3.598
r_angle_refined_deg	1.569
r_chiral_restr	0.096
r_gen_planes_other	0.015
r_bond_refined_d	0.013
r_gen_planes_refined	0.008

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.927
r_dihedral_angle_4_deg	16.702
r_dihedral_angle_3_deg	13.14
r_dihedral_angle_1_deg	6.133
r_angle_other_deg	3.598
r_angle_refined_deg	1.569
r_chiral_restr	0.096
r_gen_planes_other	0.015
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3843
Nucleic Acid Atoms
Solvent Atoms	311
Heterogen Atoms	91

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing
XDS	data processing
XSCALE	data reduction
Coot	model building

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.