2C0Y | pdb_00002c0y

THE CRYSTAL STRUCTURE OF A CYS25ALA MUTANT OF HUMAN PROCATHEPSIN S

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BY8	PDB ENTRY 1BY8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5		CRYSTALLISATION WAS PERFORMED BY THE HANGING-DROP VAPOUR DIFFUSION METHOD. EQUAL VOLUMES PROCATHEPSIN S (CYS25ALA) AT 7.0 MG/ML AND WELL SOLUTION WERE COMBINED AND PLACED OVER A WELL CONTAINING 0.1M TRIS/HCL, 0.2M MAGNESIUM ACETATE AND 20% PEG 8000, PH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.31	47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.86	α = 90
b = 140.54	β = 90
c = 78.61	γ = 90

Symmetry
Space Group	C 2 2 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	MARRESEARCH	TRIANGULAR SI (111) MONOCHROMATOR AND A CONTINUOUS BENT RH-COATED MIRROR	2001-06-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13		EMBL/DESY, HAMBURG	X13

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	2.1	30	97.9	0.09	13.4	6.4		19350		-3	24.7

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	2.1	2.14	88.5		0.47	3	4.1

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 1BY8	2.1	19.76	19350	972	97.9	0.198	0.198	0.2031	0.242	0.2549	RANDOM	28.7

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]
-0.02			-0.48		0.5

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.9
c_scangle_it	3.92
c_scbond_it	2.9
c_mcangle_it	2.53
c_mcbond_it	1.77
c_angle_deg	1.4
c_improper_angle_d	0.85
c_bond_d	0.01
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2459
Nucleic Acid Atoms
Solvent Atoms	242
Heterogen Atoms

Software

Software
Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing