1P7W | pdb_00001p7w

Crystal structure of the complex of Proteinase K with a designed heptapeptide inhibitor Pro-Ala-Pro-Phe-Ala-Ser-Ala at atomic resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1IC6	PDB ENTRY 1IC6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	microgravity with APCF reactors	6.5	295	Tris HCl, CaCl2, NaNO3, pH 6.5, microgravity with APCF reactors, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.835	α = 90
b = 67.835	β = 90
c = 101.563	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		IMAGE PLATE	MARRESEARCH	mirrors	2000-10-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.91	EMBL/DESY, HAMBURG	X11

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	1.02	20	99	0.063	24.4	15.8	119205	119205	-3	-3	5

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)
	1.02	1.06	95		0.234	5.58		11282

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1IC6	1.02	20	119205	119205	1192	99.82	0.12917	0.1291	0.12904	0.14162	RANDOM	7.92

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]
					0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	6.967
r_dihedral_angle_1_deg	6.716
r_scangle_it	3.736
r_scbond_it	2.486
r_sphericity_bonded	2.461
r_mcangle_it	1.704
r_angle_refined_deg	1.482
r_rigid_bond_restr	1.095
r_mcbond_it	1.066
r_angle_other_deg	0.919
r_symmetry_vdw_refined	0.543
r_symmetry_vdw_other	0.412
r_symmetry_hbond_refined	0.409
r_nbd_other	0.276
r_nbd_refined	0.263
r_chiral_restr	0.218
r_xyhbond_nbd_refined	0.199
r_nbtor_other	0.088
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.006
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2077
Nucleic Acid Atoms
Solvent Atoms	432
Heterogen Atoms	22

Software

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