3IOQ | pdb_00003ioq

Crystal structure of the Carica candamarcensis cysteine protease CMS1MS2 in complex with E-64.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MEG	Model predicted by SwissModel using the primary structure of CMS1MS2 and the structures of caricain (PDBID 1MEG), chymopapain (PDBID 1YAL) and papain (PDBID 1PPN)
experimental model	PDB	1YAL	Model predicted by SwissModel using the primary structure of CMS1MS2 and the structures of caricain (PDBID 1MEG), chymopapain (PDBID 1YAL) and papain (PDBID 1PPN)
experimental model	PDB	1PPN	Model predicted by SwissModel using the primary structure of CMS1MS2 and the structures of caricain (PDBID 1MEG), chymopapain (PDBID 1YAL) and papain (PDBID 1PPN)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	0.2 M ammonium sulfate, 25% PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.5	64.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.639	α = 90
b = 73.639	β = 90
c = 118.786	γ = 90

Symmetry
Space Group	P 41 21 2

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	MARMOSAIC 225 mm CCD	Vertical Collimating Mirror, DCM, Toroidal Focusing Mirror	2008-10-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	1.458	LNLS	W01B-MX2

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	1.87	62.6	100	0.081	45.8	28.1	27792	27792

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)
	1.87	1.93	100		0.251	17	27.8	2270

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	Model predicted by SwissModel using the primary structure of CMS1MS2 and the structures of caricain (PDBID 1MEG), chymopapain (PDBID 1YAL) and papain (PDBID 1PPN)	1.87	62.6	1	1	27739	27714	1395	99.91	0.164	0.164	0.162	0.1608	0.193	0.192	RANDOM	22.258

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			0.06		-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.985
r_dihedral_angle_4_deg	16.584
r_dihedral_angle_3_deg	12.412
r_dihedral_angle_1_deg	5.637
r_scangle_it	3.659
r_scbond_it	2.488
r_mcangle_it	1.458
r_angle_refined_deg	1.301
r_mcbond_it	1.238
r_nbtor_refined	0.307
r_nbd_refined	0.222
r_symmetry_hbond_refined	0.208
r_symmetry_vdw_refined	0.194
r_xyhbond_nbd_refined	0.148
r_chiral_restr	0.089
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1689
Nucleic Acid Atoms
Solvent Atoms	216
Heterogen Atoms	110

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
AMoRE	phasing