Experiment: 5KXU

Structure Proteinase K determined by SACLA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4B5L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	6.5	293	0.1 M MES-NaOH (pH 6.5), 0.5 M NaNO3, 0.1 M CaCl2

Crystal Properties
Matthews coefficient	Solvent content
2.2	43.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.5	α = 90
b = 68.5	β = 90
c = 108.4	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	CCD	MPCCD		2015-04-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SACLA BEAMLINE BL3	0.95	SACLA	BL3

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	1.23	27.15	100	11.5	1741.4		81247

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	1.23	1.25	100		0.28	835.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4B5L	1.2	27.15	1.35	81247	4028	100	0.1134	0.1126	0.1201	0.1288	0.1358

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
f_dihedral_angle_d	13.121
f_angle_d	0.873
f_chiral_restr	0.079
f_bond_d	0.009
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2032
Nucleic Acid Atoms
Solvent Atoms	215
Heterogen Atoms	6

Software

Software
Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling