2NQD | pdb_00002nqd

Crystal structure of cysteine protease inhibitor, chagasin, in complex with human cathepsin L

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NNR	PDB ENTRY 2NNR, 1CS8
experimental model	PDB	1CS8	PDB ENTRY 2NNR, 1CS8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	291	20% iso-Propanol, 20% PEG 4000, 0.1M Na Citrate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.27	α = 90
b = 50.063	β = 103.44
c = 65.008	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	MAR CCD 165 mm		2005-10-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.8078	EMBL/DESY, HAMBURG	X13

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	1.74	63.25	98.9	0.061	12.1	3.6	37938	37521		-3	18.975

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	1.74	1.81	92.5		0.399	3.3	3	3478

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	PDB ENTRY 2NNR, 1CS8	1.75	40	37938	37513	1891	98.08	0.151	0.15	0.148	0.1475	0.188	0.1855	RANDOM	21.463

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]
-0.02		0.01	-0.02		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.238
r_dihedral_angle_4_deg	17.014
r_dihedral_angle_3_deg	13.825
r_dihedral_angle_1_deg	5.942
r_scangle_it	3.429
r_scbond_it	2.159
r_angle_refined_deg	1.41
r_mcangle_it	1.391
r_mcbond_it	0.8
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.238
r_dihedral_angle_4_deg	17.014
r_dihedral_angle_3_deg	13.825
r_dihedral_angle_1_deg	5.942
r_scangle_it	3.429
r_scbond_it	2.159
r_angle_refined_deg	1.41
r_mcangle_it	1.391
r_mcbond_it	0.8
r_nbtor_refined	0.304
r_symmetry_vdw_refined	0.245
r_nbd_refined	0.204
r_symmetry_hbond_refined	0.182
r_xyhbond_nbd_refined	0.167
r_chiral_restr	0.111
r_metal_ion_refined	0.111
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2548
Nucleic Acid Atoms
Solvent Atoms	564
Heterogen Atoms	30

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

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.