2Z30 | pdb_00002z30

Crystal structure of complex form between mat-Tk-subtilisin and Tk-propeptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2E1P	PDB ENTRY 2E1P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	283	0.1M Sodium Cacodylate, 0.2M Zinc Acetate, 2% (w/v) PEG 4000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.289	α = 90
b = 68.514	β = 90
c = 73.627	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	RIGAKU JUPITER 210		2006-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.0	SPring-8	BL38B1

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	1.65	50	100	0.057	37.7			39894

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	1.65	1.71	100		0.177	6.1

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 2E1P	1.65	29.5	37822	1982	99.95	0.15289	0.15133	0.16	0.18357	0.2	RANDOM	12.961

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.757
r_dihedral_angle_1_deg	5.318
r_scangle_it	3.883
r_scbond_it	2.549
r_angle_refined_deg	1.685
r_mcangle_it	1.578
r_mcbond_it	0.967
r_angle_other_deg	0.827
r_xyhbond_nbd_other	0.487
r_symmetry_hbond_other	0.437
r_symmetry_vdw_refined	0.386
r_symmetry_hbond_refined	0.273
r_nbd_refined	0.272
r_metal_ion_refined	0.256
r_xyhbond_nbd_refined	0.219
r_nbd_other	0.21
r_symmetry_vdw_other	0.174
r_chiral_restr	0.108
r_bond_refined_d	0.019
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2827
Nucleic Acid Atoms
Solvent Atoms	486
Heterogen Atoms	8

Software

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