2R9F | pdb_00002r9f

Calpain 1 proteolytic core inactivated by ZLAK-3002, an alpha-ketoamide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KXR	pdb entry 1kxr chain A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	1.5 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
2.04	39.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.569	α = 90
b = 70.568	β = 90
c = 110.406	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	CCD	ADSC QUANTUM 210	mirrors	2007-04-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A	1.0	NSLS	X6A

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	1.6	59.46	96.6	0.078	8.4	5.6	42370	42370

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	1.6	1.69	82.6		0.602	1.6	3.1

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 1kxr chain A	1.6	35.29	40535	38914	2082	96.03	0.19057	0.18893	0.19	0.22174	0.22	RANDOM	15.802

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]
			-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.311
r_dihedral_angle_4_deg	17.414
r_dihedral_angle_3_deg	12.095
r_dihedral_angle_1_deg	5.863
r_scangle_it	2.911
r_scbond_it	1.854
r_mcangle_it	1.379
r_angle_refined_deg	1.273
r_mcbond_it	0.838
r_nbtor_refined	0.309
r_nbd_refined	0.206
r_symmetry_vdw_refined	0.177
r_symmetry_hbond_refined	0.154
r_xyhbond_nbd_refined	0.126
r_metal_ion_refined	0.108
r_chiral_restr	0.096
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
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	2594
Nucleic Acid Atoms
Solvent Atoms	268
Heterogen Atoms	54

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing