1Y4D | pdb_00001y4d

Crystal structure of the complex of subtilisin BPN' with chymotrypsin inhibitor 2 M59R/E60S mutant

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TM3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	277	potassium phosphate, PEG 8000, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.3	45.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.381	α = 90
b = 115.381	β = 90
c = 42.907	γ = 120

Symmetry
Space Group	P 61

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 4		2003-06-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.000	ALS	8.3.1

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	32.55	99.6	0.157	7.4	4.9	22160	22160		-3

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	1TM3	2	32.55	22156	21026	1130	99.16	0.19996	0.19996	0.1971	0.2	0.25207	0.25	inherited from 1TM3	26.581

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]
-0.52	-0.26		-0.52		0.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.881
r_scangle_it	4.393
r_scbond_it	2.783
r_mcangle_it	1.826
r_angle_refined_deg	1.81
r_mcbond_it	1.088
r_symmetry_hbond_refined	0.301
r_nbd_refined	0.219
r_symmetry_vdw_refined	0.206
r_xyhbond_nbd_refined	0.166

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.881
r_scangle_it	4.393
r_scbond_it	2.783
r_mcangle_it	1.826
r_angle_refined_deg	1.81
r_mcbond_it	1.088
r_symmetry_hbond_refined	0.301
r_nbd_refined	0.219
r_symmetry_vdw_refined	0.206
r_xyhbond_nbd_refined	0.166
r_chiral_restr	0.131
r_metal_ion_refined	0.083
r_bond_refined_d	0.023
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2461
Nucleic Acid Atoms
Solvent Atoms	114
Heterogen Atoms	2

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
TRUNCATE	data reduction
EPMR	phasing
REFMAC	refinement
CCP4	data scaling
TRUNCATE	data scaling

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.