4BS5 | pdb_00004bs5

MOUSE CATHEPSIN S WITH COVALENT LIGAND

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		IN HOUSE STRUCTURES

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		3.5		3 M NACL, 0.1M CITRATE PH3.5

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.64	α = 90
b = 66.79	β = 114.06
c = 54.32	γ = 90

Symmetry
Space Group	C 1 2 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	MARRESEARCH		2008-04-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA		SLS	X10SA

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	1.25	35.7	99.4	0.13	6.13	3.58		67233		-3

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	1.25	1.35	97.7		0.45	2.18	3.47

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	IN HOUSE STRUCTURES	1.25	35.69	63129	3367	98.44	0.19858	0.1971	0.21	0.22694	0.24	RANDOM	8.994

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]
0.87		-0.66	-0.66		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.196
r_sphericity_free	18.629
r_dihedral_angle_4_deg	12.516
r_dihedral_angle_3_deg	12.111
r_dihedral_angle_1_deg	5.486
r_sphericity_bonded	4.528
r_rigid_bond_restr	2.179
r_angle_refined_deg	1.492
r_angle_other_deg	0.878
r_chiral_restr	0.101
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1676
Nucleic Acid Atoms
Solvent Atoms	339
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SADABS	data scaling
PHASER	phasing