3N3G

4-(3-Trifluoromethylphenyl)-pyrimidine-2-carbonitrile as cathepsin S inhibitors: N3, not N1 is critically important

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	298	crystallisation solution: 50 mM NaAcetate, 0.25 M NaCl, 4 mM MMTS, 30% PEG 4K, 0.1 M NaCitrate, 0,2 M (NH4)2SO4, 10 mM DMSO, 10 mM DTT. Cryoprotectant composition: 30% PEG 4K, 0.1 M NaCitrate, 0.2 M (NH4)2SO4, 15% PEG 400 (+ 10% compound). Ligand was introduced by soaking crystals prepared with another compound, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.757	α = 90
b = 85.757	β = 90
c = 150.902	γ = 90

Symmetry
Space Group	P 41 2 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	RIGAKU RAXIS IV		2007-07-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	1.6	85.75	87.7	0.166	5.3	5.28		65361

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)
	1.6	1.66	24.9		0.501	1.1	1.41	1825

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.6	74.56	65283	3289	87.78	0.225	0.223	0.264	RANDOM	24.555

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]
-0.03			-0.03		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.388
r_dihedral_angle_4_deg	24.167
r_dihedral_angle_3_deg	11.873
r_dihedral_angle_1_deg	5.591
r_scangle_it	1.971
r_scbond_it	1.347
r_angle_refined_deg	1.145
r_angle_other_deg	0.871
r_mcangle_it	0.839
r_mcbond_it	0.553
r_symmetry_vdw_other	0.25
r_symmetry_vdw_refined	0.214
r_nbd_refined	0.19
r_nbd_other	0.189
r_nbtor_refined	0.18
r_symmetry_hbond_refined	0.167
r_xyhbond_nbd_refined	0.144
r_mcbond_other	0.104
r_nbtor_other	0.085
r_chiral_restr	0.062
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3372
Nucleic Acid Atoms
Solvent Atoms	512
Heterogen Atoms	100

Software

Software
Software Name	Purpose
d*TREK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction