3E4C | pdb_00003e4c

Procaspase-1 zymogen domain crystal structure

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RWX	PDB entry 1RWX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	7.5	277	0.2 M MgCl2 20% PEG 3350, pH 7.5, EVAPORATION, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.1	α = 105.95
b = 58.004	β = 119.6
c = 60.12	γ = 92.77

Symmetry
Space Group	P 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	CCD	ADSC QUANTUM 210	mirrors	2007-10-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.9779	ALS	5.0.1

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	2.05	20	97	0.058	11.2	3.1	38407	37223

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	2.05	2.12	87.4		0.414	1.9

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 (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1RWX	2.05	20	38566	35359	1861	96.61	0.204	0.204	0.2	0.21	0.263	RANDOM	36.783

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]
-0.13	2.51	0.5	3.46	3.81	-0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.087
r_dihedral_angle_3_deg	17.207
r_dihedral_angle_4_deg	16.691
r_dihedral_angle_1_deg	6.823
r_scangle_it	5.084
r_mcangle_it	4.883
r_mcbond_it	4.02
r_scbond_it	3.67
r_angle_refined_deg	1.406
r_angle_other_deg	0.803
r_mcbond_other	0.714
r_symmetry_vdw_refined	0.278
r_nbd_refined	0.213
r_symmetry_vdw_other	0.211
r_nbd_other	0.187
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.174
r_symmetry_hbond_refined	0.119
r_nbtor_other	0.085
r_chiral_restr	0.08
r_metal_ion_refined	0.071
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other	0.001
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4286
Nucleic Acid Atoms
Solvent Atoms	136
Heterogen Atoms	1

Software

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