2BD5 | pdb_00002bd5

Porcine pancreatic elastase complexed with beta-casomorphin-7 and Lys-Ser at pH 5 and immersed in pH 9 buffer for 30 seconds

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3EST

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	294	25MM SODIUM SULPHATE, 25MM SODIUM ACETATE (PH 5.0), 25 MG/ML PPE AND 17.5 MG/ML BCM7, AND THEN SOAKED WITH LYS-SER (50 MG/ML) IN 250MM SODIUM ACETATE (PH 5.0) (5 MICROLITRES) FOR 60 MIN , VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.655	α = 90
b = 57.585	β = 90
c = 74.524	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	127	IMAGE PLATE	RIGAKU RAXIS IV	OSMIC mirrors	2005-06-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.54180

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	1.8	19.7	99.9	0.046	20.3	3.4		20837			21.7

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	1.8	1.9	100		0.181	5.1	3.3	2972

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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3EST	1.8	19.7	20837	20794	1068	99.88	0.176	0.176	0.174	0.1768	0.212	0.215	RANDOM	30.249

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]
4.23			-2.86		-1.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.953
r_dihedral_angle_4_deg	23.184
r_dihedral_angle_3_deg	11.635
r_scangle_it	6.714
r_dihedral_angle_1_deg	6.462
r_scbond_it	5.363
r_mcangle_it	3.778
r_mcbond_it	2.987
r_angle_refined_deg	1.746
r_nbtor_refined	0.312
r_symmetry_vdw_refined	0.255
r_symmetry_hbond_refined	0.22
r_nbd_refined	0.211
r_chiral_restr	0.132
r_xyhbond_nbd_refined	0.132
r_metal_ion_refined	0.109
r_bond_refined_d	0.019
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1810
Nucleic Acid Atoms
Solvent Atoms	128
Heterogen Atoms	11

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling