4WQ3 | pdb_00004wq3

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

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	294	3 UL PROTEIN (10 MG/ML PEF(S), 5 MM SODIUM CACODYLATE, 2 MM EDTA, 5 MM BME, 1 MM CALCIUM CHLORIDE, PH 7.0) + 3 UL PRECIPITANT (50 MM SODIUM CACODYLATE, 12.5% PEG6000, 20 MM CALCIUM CHLORIDE, PH 7.0) + 1 UL WATER

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.56	α = 90
b = 79.31	β = 91.47
c = 57.02	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 2M		2013-03-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.920	Diamond	I04-1

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	1.79	39.65	97.6	0.071	0.043	0.994	11	3.7		40565

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	1.79	1.84	99.8		0.634	0.368	0.744	2	3.9	3101

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	4phj	1.79	39.65	38513	2031	97.49	0.1795	0.1776	0.19	0.2149	0.22	RANDOM	29.752

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]
-0.04		-0.76	0.62		-0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.992
r_dihedral_angle_4_deg	17.653
r_dihedral_angle_3_deg	15.124
r_dihedral_angle_1_deg	5.959
r_mcangle_it	2.551
r_angle_refined_deg	2.024
r_mcbond_it	1.8
r_mcbond_other	1.799
r_angle_other_deg	1.016
r_chiral_restr	0.135

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.992
r_dihedral_angle_4_deg	17.653
r_dihedral_angle_3_deg	15.124
r_dihedral_angle_1_deg	5.959
r_mcangle_it	2.551
r_angle_refined_deg	2.024
r_mcbond_it	1.8
r_mcbond_other	1.799
r_angle_other_deg	1.016
r_chiral_restr	0.135
r_bond_refined_d	0.021
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2806
Nucleic Acid Atoms
Solvent Atoms	297
Heterogen Atoms	136

Software

Software
Software Name	Purpose
Aimless	data scaling
Coot	model building
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
PHASER	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.