5N7Q | pdb_00005n7q

CRYSTAL STRUCTURE OF MATURE CATHEPSIN D FROM THE TICK IXODES RICINUS (IRCD1) IN COMPLEX WITH THE INHIBITOR PEPSTATIN A

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	291	1:1 PROTEIN (5 MG/ML IN 2.5 MM SODIUM FORMATE, 20 MM SODIUM CHLORIDE) TO RESERVOIR (0.14 M SODIUM CHLORIDE, 0.07 M BIS-TRIS, PH 5.5, 17.5% PEG3350, 1 MM DTT), CRYOCOOLED AFTER A QUICK SOAK IN RESERVOIR BUFFER + 30% PEG3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.14	α = 90
b = 82.82	β = 91.13
c = 61.39	γ = 90

Symmetry
Space Group	P 1 21 1

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	RAYONIX MX-225		2012-07-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.91841	BESSY	14.2

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	1.455	61.378	98	0.08	0.08	7.2	3		104842

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.455	1.53	98.6		0.227	0.227	3.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	FOURIER SYNTHESIS	THROUGHOUT	1.45	61.38	101593	5335	99.91	0.14629	0.14522	0.15	0.16646	0.17	RANDOM	13.814

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]
0.12		0.02	-0.12		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.09
r_dihedral_angle_4_deg	18.246
r_dihedral_angle_3_deg	11.08
r_dihedral_angle_1_deg	8.761
r_long_range_B_refined	4.842
r_long_range_B_other	4.841
r_scangle_other	2.001
r_angle_refined_deg	1.5
r_mcangle_other	1.381
r_mcangle_it	1.38
r_scbond_it	1.269
r_scbond_other	1.269
r_angle_other_deg	0.983
r_mcbond_it	0.877
r_mcbond_other	0.873
r_chiral_restr	0.088
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.007
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5219
Nucleic Acid Atoms
Solvent Atoms	1308
Heterogen Atoms	13

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling