7H66 | pdb_00007h66

THE 1.13 A CRYSTAL STRUCTURE OF HUMAN CHYMASE IN COMPLEX WITH 3-hydroxy-4-methyl-2-[naphthalen-2-yl(phenyl)methyl]-4-phenylcyclobut-2-en-1-one

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		apo structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	8.5	293	Sample of human Chymase in 50 mM MES/NaOH pH 5.5, 150mM NaCl, 1mM TCEP, 10% Glycerol) at a concentration of 11mg/ml to 14mg/ml.Add [2-[(4-methylpyridin-2-yl)amino]-2-oxoethyl] 2-methylquinoline-4-carboxylate at 10x molar ratio. The compound helps to obtain crystals but is not visible in the structures. Add 0.5 mM ZnCl2. Add inhibitor, incubate for 16h on ice. Crystallize using microbatch setups with Al's oil (Hampton Research), with total drop size 1ul with 50% protein sample, using crystallization reagent of 0.1M Tris/HCl pH 8.5, 0.2M NaCl, 25% PEG 3350.

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.71	α = 90
b = 73.71	β = 90
c = 48.6	γ = 90

Symmetry
Space Group	P 43

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	MARMOSAIC 225 mm CCD		2006-09-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.99985	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.13	73.72	83.9	0.063	0.072	11.96			81825

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.13	1.2		81	0.349	0.437

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.13	73.72	77737	4085	83.94	0.19061	0.18998	0.1901	0.20219	0.2021	RANDOM	14.424

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	34.919
r_dihedral_angle_3_deg	11.074
r_dihedral_angle_4_deg	8.193
r_dihedral_angle_1_deg	6.473
r_scangle_it	2.61
r_scbond_it	1.859
r_angle_refined_deg	1.605
r_mcangle_it	1.376
r_mcbond_it	0.877
r_nbtor_refined	0.315
r_symmetry_vdw_refined	0.219
r_nbd_refined	0.199
r_symmetry_hbond_refined	0.155
r_xyhbond_nbd_refined	0.128
r_chiral_restr	0.103
r_symmetry_metal_ion_refined	0.077
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1733
Nucleic Acid Atoms
Solvent Atoms	392
Heterogen Atoms	31

Software

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