1CPX | pdb_00001cpx

BETA FORM OF CARBOXYPEPTIDASE A (RESIDUES 3-307) FROM BOVINE PANCREAS IN AN ORTHORHOMBIC CRYSTAL FORM WITH TWO ZINC IONS IN THE ACTIVE SITE.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5CPA	5CPA WITHOUT WATERS AND ZN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICRODIALYSIS	7.5		CPA FROM SIGMA #C0261 WAS DISSOLVED IN 1.0 M LICL WITH 20 MM TRIS-HCL PH 7.5 TO GIVE 12 MG/ML AND USED WITHOUT FURTHER PURIFICATION. THIS PROTEIN SOLUTION WAS PLACED IN 50 MICROL DIALYSIS BUTTONS FROM HAMPTON RESEARCH AND DIALYZED AGAINST A 2 ML RESERVOIR OF THE ABOVE MENTIONED BUFFER WHILE LOWERING THE EXTERNAL LICL CONCENTRATION BY 25% EVERY OTHER DAY. THE CRYSTALS APPEARED A~0.24 M LICL AND WAS STORED AT 0.30M LICL. IF THIS PROCEDURE DOES NOT WORK BY ITSELF AND YOU END UP WITH THE MONOCLINIC ALPHA-FORM (1-307), YOU CAN TRY TO AD TRACES OF TRYPSIN (~10 MICROG/ML) TO THE PROTEIN SOLUTION TO PROVOKE FORMATION OF THE BETA-FORM (3-307), micro dialysis

Crystal Properties
Matthews coefficient	Solvent content
2.25	45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.79	α = 90
b = 66.85	β = 90
c = 96.02	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	290	IMAGE PLATE	RIGAKU RAXIS II		1996-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	40	94.1	0.038	0.038	30.7	4.3		20453			19

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2	2.03	67.7		0.157	0.157	7.1	3.9

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	5CPA WITHOUT WATERS AND ZN	2	8	20060	977	93.4	0.167	0.167	0.15	0.226	0.21	RANDOM	15.8

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
x_dihedral_angle_d	22.4
x_scbond_it	2.876
x_scangle_it	2.8
x_mcangle_it	2.277
x_mcbond_it	2.221
x_angle_deg	2.001
x_improper_angle_d	1.238
x_bond_d	0.01
x_bond_d_na
x_bond_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2421
Nucleic Acid Atoms
Solvent Atoms	277
Heterogen Atoms	3

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
X-PLOR	refinement

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.