2PQ2 | pdb_00002pq2

Structure of serine proteinase K complex with a highly flexible hydrophobic peptide at 1.8A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DP4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	298	0.2M AMMONIUM ACTATE, 0.1M SODIUM ACETATE, 30% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.314	α = 90
b = 68.314	β = 90
c = 108.418	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	IMAGE PLATE	MARRESEARCH	MIRROR	2007-02-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418

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	1.82	57.3	99.6	0.0561	12.2		24800	23699

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.82	1.87	97.6		0.261	2

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	2DP4	1.82	57.3	23699	22483	1216	99.89	0.17211	0.17016	0.16823	0.18	0.20728	0.17	RANDOM	18.46

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]
-0.08			-0.08		0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.328
r_dihedral_angle_4_deg	19.915
r_dihedral_angle_3_deg	12.832
r_dihedral_angle_1_deg	5.648
r_scangle_it	3.221
r_scbond_it	2.104
r_angle_refined_deg	1.224
r_mcangle_it	1.142
r_mcbond_it	0.671
r_nbtor_refined	0.324

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.328
r_dihedral_angle_4_deg	19.915
r_dihedral_angle_3_deg	12.832
r_dihedral_angle_1_deg	5.648
r_scangle_it	3.221
r_scbond_it	2.104
r_angle_refined_deg	1.224
r_mcangle_it	1.142
r_mcbond_it	0.671
r_nbtor_refined	0.324
r_nbd_refined	0.308
r_symmetry_vdw_refined	0.181
r_symmetry_hbond_refined	0.168
r_xyhbond_nbd_refined	0.132
r_chiral_restr	0.077
r_metal_ion_refined	0.069
r_bond_refined_d	0.012
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2089
Nucleic Acid Atoms
Solvent Atoms	263
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
AUTOMAR	data reduction
SCALEPACK	data scaling
AMoRE	phasing

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.