3HHA | pdb_00003hha

Crystal structure of cathepsin L in complex with AZ12878478

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.4	293	PEG, pH 7.4, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.26	α = 105.6
b = 62.69	β = 93.22
c = 68.24	γ = 115.55

Symmetry
Space Group	P 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	PIXEL	PSI PILATUS 6M	LN2 cooled fixed-exit	2007-10-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0000	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.27	44.28	85.6	0.034		1.5	182842	182842

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	1.27	1.33	65.8		0.098		0.4

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 (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	FOURIER SYNTHESIS	THROUGHOUT	1.27	44.28	173697	9143	100	0.11672	0.11812	0.11632	0.12	0.15237	0.15	RANDOM	12.158

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]
-0.34	-0.25	-0.05	0.26	-0.6	-0.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.701
r_sphericity_free	12.266
r_dihedral_angle_4_deg	11.519
r_dihedral_angle_3_deg	11.187
r_sphericity_bonded	6.143
r_dihedral_angle_1_deg	5.89
r_scangle_it	5.842
r_scbond_it	4.779
r_mcangle_it	3.528
r_mcbond_it	3.102
r_rigid_bond_restr	2.449
r_mcbond_other	1.798
r_angle_refined_deg	1.355
r_angle_other_deg	0.81
r_symmetry_hbond_refined	0.369
r_symmetry_vdw_other	0.269
r_nbd_refined	0.229
r_xyhbond_nbd_refined	0.204
r_nbd_other	0.19
r_symmetry_vdw_refined	0.189
r_nbtor_refined	0.185
r_chiral_restr	0.089
r_nbtor_other	0.086
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6695
Nucleic Acid Atoms
Solvent Atoms	993
Heterogen Atoms	145

Software

Software
Software Name	Purpose
XDL	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling