5D69 | pdb_00005d69

Human calpain PEF(S) with (2Z,2Z')-2,2'-disulfanediylbis(3-(6-iodoindol-3-yl)acrylic acid) bound

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	12% PEG6000, 20 MM CACL2, 50 MM CACODYLATE BUFFER, PH7.4

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.03	α = 90
b = 79.65	β = 91.81
c = 57.16	γ = 90

Symmetry
Space Group	P 1 21 1

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		2015-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	.97623	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim 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	1.97	34.47	98.4	0.072	0.043	0.996	9.5	3.6		31256

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.97	2.02	99		0.886	0.519	0.716	1.4	3.8	2325

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.97	34.47	29754	1482	98.33	0.2006	0.1989	0.2	0.2343	0.24	RANDOM	49.919

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]
0.52		-0.85			-0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.686
r_dihedral_angle_4_deg	19.007
r_dihedral_angle_3_deg	17.162
r_dihedral_angle_1_deg	6.141
r_angle_refined_deg	1.963
r_mcangle_it	1.938
r_angle_other_deg	1.453
r_mcbond_it	1.202
r_mcbond_other	1.2
r_chiral_restr	0.138

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.686
r_dihedral_angle_4_deg	19.007
r_dihedral_angle_3_deg	17.162
r_dihedral_angle_1_deg	6.141
r_angle_refined_deg	1.963
r_mcangle_it	1.938
r_angle_other_deg	1.453
r_mcbond_it	1.202
r_mcbond_other	1.2
r_chiral_restr	0.138
r_bond_refined_d	0.019
r_gen_planes_refined	0.01
r_bond_other_d	0.007
r_gen_planes_other	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2806
Nucleic Acid Atoms
Solvent Atoms	115
Heterogen Atoms	117

Software

Software
Software Name	Purpose
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
xia2	data reduction

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.