2I7A | pdb_00002i7a

Domain IV of Human Calpain 13

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	298	25% PEG4K, 0.2M NH4SO4, 0.1M Na-Ac, 10 mg/mL protein solution, cryoprotected with 25% glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.115	α = 90
b = 86.115	β = 90
c = 47.417	γ = 120

Symmetry
Space Group	P 32 2 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	IMAGE PLATE	RIGAKU RAXIS IV++		2006-08-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.8	19	99	0.091	33.18	9.6	18860	18860		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.86	89.6		0.88	1.2	3.3	1684

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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 1KFU	1.8	19	18860	17908	952	98.91	0.17054	0.16918	0.1736	0.19699	0.2001	RANDOM	37.105

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]
-1.06	-0.53		-1.06		1.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.486
r_dihedral_angle_4_deg	17.322
r_dihedral_angle_3_deg	12.187
r_dihedral_angle_1_deg	4.877
r_scangle_it	4.868
r_scbond_it	3.654
r_mcangle_it	2.668
r_mcbond_it	2.104
r_angle_refined_deg	1.496
r_nbtor_refined	0.309
r_symmetry_hbond_refined	0.247
r_nbd_refined	0.222
r_symmetry_vdw_refined	0.186
r_xyhbond_nbd_refined	0.181
r_chiral_restr	0.107
r_metal_ion_refined	0.063
r_bond_refined_d	0.017
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1268
Nucleic Acid Atoms
Solvent Atoms	92
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing