3BOW

Structure of M-calpain in complex with Calpastatin

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KFU	PDB ENTRY 1KFU PDB ENTRY 1TL9
experimental model	PDB	1TL9	PDB ENTRY 1KFU PDB ENTRY 1TL9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5	298	pH 6.5, microbatch under paraffin oil, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.12	42.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.477	α = 90
b = 66.985	β = 100.76
c = 108.656	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	CCD	ADSC QUANTUM 210	MIRRORS	2007-04-24		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A		NSLS	X6A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.4	66.965	96.7	0.084	0.084	7.7	3.6		36208			34.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.53	82.5		0.317	0.317	2.2	3.1

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1KFU PDB ENTRY 1TL9	2.4	66.23	34375	1819	96.47	0.20062	0.19756	0.25784	RANDOM	11.827

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]
0.48		-0.33	0.22		-0.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.765
r_dihedral_angle_3_deg	17.628
r_dihedral_angle_4_deg	13.445
r_dihedral_angle_1_deg	6.138
r_scangle_it	1.919
r_angle_refined_deg	1.237
r_scbond_it	1.166
r_mcangle_it	0.841
r_mcbond_it	0.51
r_nbtor_refined	0.299
r_nbd_refined	0.203
r_symmetry_vdw_refined	0.187
r_xyhbond_nbd_refined	0.144
r_metal_ion_refined	0.122
r_symmetry_hbond_refined	0.115
r_chiral_restr	0.086
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7396
Nucleic Acid Atoms
Solvent Atoms	176
Heterogen Atoms	10

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction