1YU6 | pdb_00001yu6

Crystal Structure of the Subtilisin Carlsberg:OMTKY3 Complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VSB	1VSB and 1CHO
experimental model	PDB	1CHO	1VSB and 1CHO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.1	298	10% ethylene glycol, 480 mM sodium malate, 75 mM sodium citrate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.256	α = 90
b = 100.971	β = 90
c = 115.785	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	ADSC QUANTUM 4	Mirrors	2003-07-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	1.00	ALS	5.0.3

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	1.55	74.54	95.4	0.102	0.266	14.7	6.4	88530	88530	1.5	3

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)
	1.55	1.61	77.3		0.422	3.21	5.1	7071

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	1VSB and 1CHO	1.55	74.54	88530	84093	4428	85.69	0.19199	0.19199	0.19129	0.2	0.20518	0.22	RANDOM	12.112

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]
0.47			-0.78		0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.587
r_scangle_it	3.189
r_scbond_it	1.929
r_angle_refined_deg	1.598
r_angle_other_deg	1.152
r_mcangle_it	1.061
r_mcbond_it	0.551
r_symmetry_hbond_refined	0.205
r_nbd_other	0.202
r_nbd_refined	0.187
r_symmetry_vdw_other	0.18
r_xyhbond_nbd_refined	0.175
r_symmetry_vdw_refined	0.117
r_chiral_restr	0.101
r_metal_ion_refined	0.087
r_nbtor_other	0.083
r_bond_refined_d	0.016
r_bond_other_d	0.011
r_gen_planes_other	0.006
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4607
Nucleic Acid Atoms
Solvent Atoms	329
Heterogen Atoms	2

Software

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