2NQI | pdb_00002nqi

Calpain 1 proteolytic core inactivated by WR13(R,R), an epoxysuccinyl-type inhibitor.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2G8J	PDB entry 2G8J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	Expansion around 1.1-1.7 M NaCl, 10 mM CaCl2, and 0.1 M MES (pH 6.0), VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.369	α = 90
b = 70.06	β = 90
c = 110.743	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARRESEARCH	OSMIC CONFOCAL MIRROR	2006-05-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	2.04	59.3	99.3	0.139	11			19556			17.3

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)
	2.04	2.12	72.4		0.456	3.1		2235

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 2G8J	2.04	59.23	15556	1057	99.34	0.1841	0.18066	0.18	0.24735	0.24	RANDOM	16.674

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]
-0.06			0.07		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.553
r_dihedral_angle_4_deg	20.481
r_dihedral_angle_3_deg	14.988
r_dihedral_angle_1_deg	6.689
r_scangle_it	3.684
r_scbond_it	2.53
r_mcangle_it	1.762
r_angle_refined_deg	1.659
r_mcbond_it	1.088
r_nbtor_refined	0.312
r_symmetry_vdw_refined	0.283
r_symmetry_hbond_refined	0.281
r_nbd_refined	0.223
r_xyhbond_nbd_refined	0.181
r_chiral_restr	0.121
r_metal_ion_refined	0.081
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
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	2634
Nucleic Acid Atoms
Solvent Atoms	153
Heterogen Atoms	45

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing