3DF0 | pdb_00003df0

Calcium-dependent complex between m-calpain and calpastatin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MDW	PDB ENTRY 1MDW, 1DF0 domain III and DIV and 1DVI
experimental model	PDB	1DF0	PDB ENTRY 1MDW, 1DF0 domain III and DIV and 1DVI
experimental model	PDB	1DVI	PDB ENTRY 1MDW, 1DF0 domain III and DIV and 1DVI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	298	4-9% PEG 3350, 5-10 mM CaCl2, 50-100 mM NaOAc (pH 5.5) , VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 147.39	α = 90
b = 147.39	β = 90
c = 47.222	γ = 90

Symmetry
Space Group	P 42

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 315		2007-07-02	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 315			M	SINGLE WAVELENGTH
3	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD			M	SINGLE WAVELENGTH
4	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD			M	SINGLE WAVELENGTH
1,2,3,4	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	0.98064	ALS	5.0.3
2	SYNCHROTRON	NSLS BEAMLINE X29A	0.98064	NSLS	X29A
3	SYNCHROTRON	APS BEAMLINE 22-ID	0.98064	APS	22-ID
4	SYNCHROTRON	APS BEAMLINE 22-BM	0.98064	APS	22-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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
1,2,3,4	2.95	49.25		0.096	21.4	4.4		20755		2	92

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2,3,4	2.95	3.06			0.82	2.1	4.2

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	PDB ENTRY 1MDW, 1DF0 domain III and DIV and 1DVI	2.95	49.15	20755	1164	99.83	0.232	0.229	0.22	0.299	0.3	RANDOM	94.719

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]
-0.62			-0.62		1.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.977
r_dihedral_angle_3_deg	22.028
r_angle_other_deg	16.358
r_dihedral_angle_4_deg	15.986
r_dihedral_angle_1_deg	7.187
r_scangle_it	1.975
r_angle_refined_deg	1.485
r_scbond_it	1.208
r_mcangle_it	0.904
r_mcbond_it	0.53
r_symmetry_hbond_refined	0.345
r_nbtor_other	0.32
r_nbtor_refined	0.318
r_nbd_other	0.313
r_nbd_refined	0.252
r_xyhbond_nbd_refined	0.179
r_metal_ion_refined	0.172
r_symmetry_vdw_refined	0.159
r_chiral_restr	0.108
r_mcbond_other	0.088
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7290
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	10

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection